diff --git a/bin/martinize2 b/bin/martinize2 index 38612bb50..91eca3261 100755 --- a/bin/martinize2 +++ b/bin/martinize2 @@ -472,7 +472,7 @@ def entry(): "-ef", dest="rb_force_constant", type=float, - default=500, + default=700, help="Elastic bond force constant Fc in kJ/mol/nm^2", ) rb_group.add_argument( @@ -625,18 +625,25 @@ def entry(): prot_group = parser.add_argument_group("Protein description") + prot_group.add_argument( + "-noscfix", + dest="noscfix", + action="store_true", + default=False, + help="Don't apply side chain corrections. Please note the change in behaviour from martinize v0.11.0", + ) prot_group.add_argument( "-scfix", dest="scfix", action="store_true", - default=False, - help="Apply side chain corrections.", + help="Old -scfix argument. Side chain fixes are now assumed by default, and the flag does not need" + " to be specified. Will be deprecated in future." ) prot_group.add_argument( "-cys", dest="cystein_bridge", type=_cys_argument, - default="none", + default="auto", help="Cystein bonds", ) prot_group.add_argument( @@ -923,14 +930,23 @@ def entry(): type="missing-feature", ) vermouth.SetMoleculeMeta(extdih=args.extdih).run_system(system) - if args.scfix and not target_ff.has_feature("scfix"): + if args.scfix: + LOGGER.warning( + "The scfix argument has been deprecated and will be removed in the future. " + "Side chain fixing is now assumed by default, so no flag needs to be " + "passed. If you do not want side chain fixes to be applied, the -noscfix " + "flag can be used." + ) + scfix = not args.noscfix + if scfix and not target_ff.has_feature("scfix"): LOGGER.warning( 'The force field "{}" does not define angle and ' - "torsion for the side chain corrections (-scfix).", + "torsion for the side chain corrections." + " If intended, please specify -noscfix explicitly", target_ff.name, type="missing-feature", ) - vermouth.SetMoleculeMeta(scfix=args.scfix).run_system(system) + vermouth.SetMoleculeMeta(scfix=scfix).run_system(system) vermouth.SetMoleculeMeta(idr=args.idr_tune).run_system(system) if args.idr_tune: diff --git a/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/command b/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/command index 4e096bade..e9c7bcecd 100644 --- a/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/command @@ -4,3 +4,4 @@ martinize2 -o topol.top -ff martini3001 -nt +-noscfix diff --git a/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/command b/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/command index 5d4540377..366dc838e 100644 --- a/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/command @@ -5,3 +5,4 @@ martinize2 -ff martini22 -dssp -cys auto +-noscfix diff --git a/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command b/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command index 3410e70ed..1717f0f60 100644 --- a/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command @@ -6,3 +6,5 @@ martinize2 -ss CCSHHHHHHHHHHCCCCHHHHHHHHHHHTSCHHHHHHHTCCCC -nter NH2-ter -cter COOH-ter +-ef 500 +-noscfix diff --git a/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/command b/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/command index b2182ed04..10ddca0e9 100644 --- a/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/command @@ -6,3 +6,4 @@ martinize2 -dssp -eu 0.7 -ef 800.0 +-noscfix diff --git a/vermouth/tests/data/integration_tests/tier-1/1UBQ/README b/vermouth/tests/data/integration_tests/tier-1/1UBQ/README new file mode 100644 index 000000000..3caaa996d --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/1UBQ/README @@ -0,0 +1,11 @@ +### DETAILS: + +# Ubiquitin 1UBQ + +### testing 'new' defaults after -scfix and -ef behaviour changed + +### TEST: + +# -ff martini 3001 +# no -scfix +# diff --git a/vermouth/tests/data/integration_tests/tier-1/1UBQ/aa.pdb b/vermouth/tests/data/integration_tests/tier-1/1UBQ/aa.pdb new file mode 100644 index 000000000..2beb2727c --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/1UBQ/aa.pdb @@ -0,0 +1,983 @@ +HEADER CHROMOSOMAL PROTEIN 02-JAN-87 1UBQ +TITLE STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION +COMPND MOL_ID: 1; +COMPND 2 MOLECULE: UBIQUITIN; +COMPND 3 CHAIN: A; +COMPND 4 ENGINEERED: YES +SOURCE MOL_ID: 1; +SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; +SOURCE 3 ORGANISM_COMMON: HUMAN; +SOURCE 4 ORGANISM_TAXID: 9606 +KEYWDS CHROMOSOMAL PROTEIN +EXPDTA X-RAY DIFFRACTION +AUTHOR S.VIJAY-KUMAR,C.E.BUGG,W.J.COOK +REVDAT 5 09-MAR-11 1UBQ 1 REMARK +REVDAT 4 24-FEB-09 1UBQ 1 VERSN +REVDAT 3 01-APR-03 1UBQ 1 JRNL +REVDAT 2 16-JUL-87 1UBQ 1 JRNL REMARK +REVDAT 1 16-APR-87 1UBQ 0 +JRNL AUTH S.VIJAY-KUMAR,C.E.BUGG,W.J.COOK +JRNL TITL STRUCTURE OF UBIQUITIN REFINED AT 1.8 A RESOLUTION. +JRNL REF J.MOL.BIOL. V. 194 531 1987 +JRNL REFN ISSN 0022-2836 +JRNL PMID 3041007 +JRNL DOI 10.1016/0022-2836(87)90679-6 +REMARK 1 +REMARK 1 REFERENCE 1 +REMARK 1 AUTH S.VIJAY-KUMAR,C.E.BUGG,K.D.WILKINSON,R.D.VIERSTRA, +REMARK 1 AUTH 2 P.M.HATFIELD,W.J.COOK +REMARK 1 TITL COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF HUMAN, +REMARK 1 TITL 2 YEAST, AND OAT UBIQUITIN +REMARK 1 REF J.BIOL.CHEM. V. 262 6396 1987 +REMARK 1 REFN ISSN 0021-9258 +REMARK 1 REFERENCE 2 +REMARK 1 AUTH S.VIJAY-KUMAR,C.E.BUGG,K.D.WILKINSON,W.J.COOK +REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF UBIQUITIN AT 2.8 ANGSTROMS +REMARK 1 TITL 2 RESOLUTION +REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 82 3582 1985 +REMARK 1 REFN ISSN 0027-8424 +REMARK 1 REFERENCE 3 +REMARK 1 AUTH W.J.COOK,F.L.SUDDATH,C.E.BUGG,G.GOLDSTEIN +REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY INVESTIGATION OF +REMARK 1 TITL 2 UBIQUITIN, A NON-HISTONE CHROMOSOMAL PROTEIN +REMARK 1 REF J.MOL.BIOL. V. 130 353 1979 +REMARK 1 REFN ISSN 0022-2836 +REMARK 1 REFERENCE 4 +REMARK 1 AUTH D.H.SCHLESINGER,G.GOLDSTEIN +REMARK 1 TITL MOLECULAR CONSERVATION OF 74 AMINO ACID SEQUENCE OF +REMARK 1 TITL 2 UBIQUITIN BETWEEN CATTLE AND MAN +REMARK 1 REF NATURE V. 255 423 1975 +REMARK 1 REFN ISSN 0028-0836 +REMARK 2 +REMARK 2 RESOLUTION. 1.80 ANGSTROMS. +REMARK 3 +REMARK 3 REFINEMENT. +REMARK 3 PROGRAM : PROLSQ +REMARK 3 AUTHORS : KONNERT,HENDRICKSON +REMARK 3 +REMARK 3 DATA USED IN REFINEMENT. +REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 +REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL +REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL +REMARK 3 COMPLETENESS FOR RANGE (%) : NULL +REMARK 3 NUMBER OF REFLECTIONS : NULL +REMARK 3 +REMARK 3 FIT TO DATA USED IN REFINEMENT. +REMARK 3 CROSS-VALIDATION METHOD : NULL +REMARK 3 FREE R VALUE TEST SET SELECTION : NULL +REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 +REMARK 3 R VALUE (WORKING SET) : NULL +REMARK 3 FREE R VALUE : NULL +REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL +REMARK 3 FREE R VALUE TEST SET COUNT : NULL +REMARK 3 +REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. +REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL +REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL +REMARK 3 FREE R VALUE (NO CUTOFF) : NULL +REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL +REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL +REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL +REMARK 3 +REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. +REMARK 3 PROTEIN ATOMS : 602 +REMARK 3 NUCLEIC ACID ATOMS : 0 +REMARK 3 HETEROGEN ATOMS : 0 +REMARK 3 SOLVENT ATOMS : 58 +REMARK 3 +REMARK 3 B VALUES. +REMARK 3 FROM WILSON PLOT (A**2) : NULL +REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL +REMARK 3 OVERALL ANISOTROPIC B VALUE. +REMARK 3 B11 (A**2) : NULL +REMARK 3 B22 (A**2) : NULL +REMARK 3 B33 (A**2) : NULL +REMARK 3 B12 (A**2) : NULL +REMARK 3 B13 (A**2) : NULL +REMARK 3 B23 (A**2) : NULL +REMARK 3 +REMARK 3 ESTIMATED COORDINATE ERROR. +REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL +REMARK 3 ESD FROM SIGMAA (A) : NULL +REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL +REMARK 3 +REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. +REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA +REMARK 3 BOND LENGTH (A) : 0.016 ; NULL +REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL +REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL +REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL +REMARK 3 +REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL +REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL +REMARK 3 +REMARK 3 NON-BONDED CONTACT RESTRAINTS. +REMARK 3 SINGLE TORSION (A) : NULL ; NULL +REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL +REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL +REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL +REMARK 3 +REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. +REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL +REMARK 3 PLANAR (DEGREES) : NULL ; NULL +REMARK 3 STAGGERED (DEGREES) : NULL ; NULL +REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL +REMARK 3 +REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA +REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL +REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL +REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL +REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL +REMARK 3 +REMARK 3 OTHER REFINEMENT REMARKS: NULL +REMARK 4 +REMARK 4 1UBQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 +REMARK 100 +REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. +REMARK 200 +REMARK 200 EXPERIMENTAL DETAILS +REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION +REMARK 200 DATE OF DATA COLLECTION : NULL +REMARK 200 TEMPERATURE (KELVIN) : NULL +REMARK 200 PH : NULL +REMARK 200 NUMBER OF CRYSTALS USED : NULL +REMARK 200 +REMARK 200 SYNCHROTRON (Y/N) : NULL +REMARK 200 RADIATION SOURCE : NULL +REMARK 200 BEAMLINE : NULL +REMARK 200 X-RAY GENERATOR MODEL : NULL +REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL +REMARK 200 WAVELENGTH OR RANGE (A) : NULL +REMARK 200 MONOCHROMATOR : NULL +REMARK 200 OPTICS : NULL +REMARK 200 +REMARK 200 DETECTOR TYPE : NULL +REMARK 200 DETECTOR MANUFACTURER : NULL +REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL +REMARK 200 DATA SCALING SOFTWARE : NULL +REMARK 200 +REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL +REMARK 200 RESOLUTION RANGE HIGH (A) : NULL +REMARK 200 RESOLUTION RANGE LOW (A) : NULL +REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL +REMARK 200 +REMARK 200 OVERALL. +REMARK 200 COMPLETENESS FOR RANGE (%) : NULL +REMARK 200 DATA REDUNDANCY : NULL +REMARK 200 R MERGE (I) : NULL +REMARK 200 R SYM (I) : NULL +REMARK 200 FOR THE DATA SET : NULL +REMARK 200 +REMARK 200 IN THE HIGHEST RESOLUTION SHELL. +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL +REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL +REMARK 200 COMPLETENESS FOR SHELL (%) : NULL +REMARK 200 DATA REDUNDANCY IN SHELL : NULL +REMARK 200 R MERGE FOR SHELL (I) : NULL +REMARK 200 R SYM FOR SHELL (I) : NULL +REMARK 200 FOR SHELL : NULL +REMARK 200 +REMARK 200 DIFFRACTION PROTOCOL: NULL +REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL +REMARK 200 SOFTWARE USED: NULL +REMARK 200 STARTING MODEL: NULL +REMARK 200 +REMARK 200 REMARK: NULL +REMARK 280 +REMARK 280 CRYSTAL +REMARK 280 SOLVENT CONTENT, VS (%): 32.94 +REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 +REMARK 280 +REMARK 280 CRYSTALLIZATION CONDITIONS: NULL +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY +REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 +REMARK 290 +REMARK 290 SYMOP SYMMETRY +REMARK 290 NNNMMM OPERATOR +REMARK 290 1555 X,Y,Z +REMARK 290 2555 -X+1/2,-Y,Z+1/2 +REMARK 290 3555 -X,Y+1/2,-Z+1/2 +REMARK 290 4555 X+1/2,-Y+1/2,-Z +REMARK 290 +REMARK 290 WHERE NNN -> OPERATOR NUMBER +REMARK 290 MMM -> TRANSLATION VECTOR +REMARK 290 +REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS +REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM +REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY +REMARK 290 RELATED MOLECULES. +REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 25.42000 +REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 +REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.47500 +REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 +REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.38500 +REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 14.47500 +REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.42000 +REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.38500 +REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 +REMARK 290 +REMARK 290 REMARK: NULL +REMARK 300 +REMARK 300 BIOMOLECULE: 1 +REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM +REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN +REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON +REMARK 300 BURIED SURFACE AREA. +REMARK 350 +REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN +REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE +REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS +REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND +REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. +REMARK 350 +REMARK 350 BIOMOLECULE: 1 +REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC +REMARK 350 APPLY THE FOLLOWING TO CHAINS: A +REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 +REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 +REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: CLOSE CONTACTS +REMARK 500 +REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC +REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 +REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A +REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 +REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE +REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. +REMARK 500 +REMARK 500 DISTANCE CUTOFF: +REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS +REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS +REMARK 500 +REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE +REMARK 500 OE2 GLU A 16 NH1 ARG A 72 1554 2.02 +REMARK 500 NZ LYS A 48 OXT GLY A 76 4467 2.16 +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 500 +REMARK 500 GEOMETRY AND STEREOCHEMISTRY +REMARK 500 SUBTOPIC: COVALENT BOND ANGLES +REMARK 500 +REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES +REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE +REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN +REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). +REMARK 500 +REMARK 500 STANDARD TABLE: +REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) +REMARK 500 +REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 +REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 +REMARK 500 +REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 +REMARK 500 LEU A 15 CA - CB - CG ANGL. DEV. = 14.0 DEGREES +REMARK 500 ARG A 54 CD - NE - CZ ANGL. DEV. = 12.4 DEGREES +REMARK 500 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES +REMARK 500 +REMARK 500 REMARK: NULL +REMARK 525 +REMARK 525 SOLVENT +REMARK 525 +REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT +REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST +REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT +REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE +REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; +REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE +REMARK 525 NUMBER; I=INSERTION CODE): +REMARK 525 +REMARK 525 M RES CSSEQI +REMARK 525 HOH A 93 DISTANCE = 5.65 ANGSTROMS +REMARK 525 HOH A 114 DISTANCE = 5.45 ANGSTROMS +REMARK 525 HOH A 126 DISTANCE = 5.71 ANGSTROMS +DBREF 1UBQ A 1 76 UNP P62988 UBIQ_HUMAN 1 76 +SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE +SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL +SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP +SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP +SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER +SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY +FORMUL 2 HOH *58(H2 O) +HELIX 1 H1 ILE A 23 GLU A 34 1 12 +HELIX 2 H2 LEU A 56 TYR A 59 5 4 +SHEET 1 BET 5 GLY A 10 VAL A 17 0 +SHEET 2 BET 5 MET A 1 THR A 7 -1 +SHEET 3 BET 5 GLU A 64 ARG A 72 1 +SHEET 4 BET 5 GLN A 40 PHE A 45 -1 +SHEET 5 BET 5 LYS A 48 LEU A 50 -1 +CRYST1 50.840 42.770 28.950 90.00 90.00 90.00 P 21 21 21 4 +ORIGX1 1.000000 0.000000 0.000000 0.00000 +ORIGX2 0.000000 1.000000 0.000000 0.00000 +ORIGX3 0.000000 0.000000 1.000000 0.00000 +SCALE1 0.019670 0.000000 0.000000 0.00000 +SCALE2 0.000000 0.023381 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.034542 0.00000 +ATOM 1 N MET A 1 27.340 24.430 2.614 1.00 9.67 N +ATOM 2 CA MET A 1 26.266 25.413 2.842 1.00 10.38 C +ATOM 3 C MET A 1 26.913 26.639 3.531 1.00 9.62 C +ATOM 4 O MET A 1 27.886 26.463 4.263 1.00 9.62 O +ATOM 5 CB MET A 1 25.112 24.880 3.649 1.00 13.77 C +ATOM 6 CG MET A 1 25.353 24.860 5.134 1.00 16.29 C +ATOM 7 SD MET A 1 23.930 23.959 5.904 1.00 17.17 S +ATOM 8 CE MET A 1 24.447 23.984 7.620 1.00 16.11 C +ATOM 9 N GLN A 2 26.335 27.770 3.258 1.00 9.27 N +ATOM 10 CA GLN A 2 26.850 29.021 3.898 1.00 9.07 C +ATOM 11 C GLN A 2 26.100 29.253 5.202 1.00 8.72 C +ATOM 12 O GLN A 2 24.865 29.024 5.330 1.00 8.22 O +ATOM 13 CB GLN A 2 26.733 30.148 2.905 1.00 14.46 C +ATOM 14 CG GLN A 2 26.882 31.546 3.409 1.00 17.01 C +ATOM 15 CD GLN A 2 26.786 32.562 2.270 1.00 20.10 C +ATOM 16 OE1 GLN A 2 27.783 33.160 1.870 1.00 21.89 O +ATOM 17 NE2 GLN A 2 25.562 32.733 1.806 1.00 19.49 N +ATOM 18 N ILE A 3 26.849 29.656 6.217 1.00 5.87 N +ATOM 19 CA ILE A 3 26.235 30.058 7.497 1.00 5.07 C +ATOM 20 C ILE A 3 26.882 31.428 7.862 1.00 4.01 C +ATOM 21 O ILE A 3 27.906 31.711 7.264 1.00 4.61 O +ATOM 22 CB ILE A 3 26.344 29.050 8.645 1.00 6.55 C +ATOM 23 CG1 ILE A 3 27.810 28.748 8.999 1.00 4.72 C +ATOM 24 CG2 ILE A 3 25.491 27.771 8.287 1.00 5.58 C +ATOM 25 CD1 ILE A 3 27.967 28.087 10.417 1.00 10.83 C +ATOM 26 N PHE A 4 26.214 32.097 8.771 1.00 4.55 N +ATOM 27 CA PHE A 4 26.772 33.436 9.197 1.00 4.68 C +ATOM 28 C PHE A 4 27.151 33.362 10.650 1.00 5.30 C +ATOM 29 O PHE A 4 26.350 32.778 11.395 1.00 5.58 O +ATOM 30 CB PHE A 4 25.695 34.498 8.946 1.00 4.83 C +ATOM 31 CG PHE A 4 25.288 34.609 7.499 1.00 7.97 C +ATOM 32 CD1 PHE A 4 24.147 33.966 7.038 1.00 6.69 C +ATOM 33 CD2 PHE A 4 26.136 35.346 6.640 1.00 8.34 C +ATOM 34 CE1 PHE A 4 23.812 34.031 5.677 1.00 9.10 C +ATOM 35 CE2 PHE A 4 25.810 35.392 5.267 1.00 10.61 C +ATOM 36 CZ PHE A 4 24.620 34.778 4.853 1.00 8.90 C +ATOM 37 N VAL A 5 28.260 33.943 11.096 1.00 4.44 N +ATOM 38 CA VAL A 5 28.605 33.965 12.503 1.00 3.87 C +ATOM 39 C VAL A 5 28.638 35.461 12.900 1.00 4.93 C +ATOM 40 O VAL A 5 29.522 36.103 12.320 1.00 6.84 O +ATOM 41 CB VAL A 5 29.963 33.317 12.814 1.00 2.99 C +ATOM 42 CG1 VAL A 5 30.211 33.394 14.304 1.00 5.28 C +ATOM 43 CG2 VAL A 5 29.957 31.838 12.352 1.00 9.13 C +ATOM 44 N LYS A 6 27.751 35.867 13.740 1.00 6.04 N +ATOM 45 CA LYS A 6 27.691 37.315 14.143 1.00 6.12 C +ATOM 46 C LYS A 6 28.469 37.475 15.420 1.00 6.57 C +ATOM 47 O LYS A 6 28.213 36.753 16.411 1.00 5.76 O +ATOM 48 CB LYS A 6 26.219 37.684 14.307 1.00 7.45 C +ATOM 49 CG LYS A 6 25.884 39.139 14.615 1.00 11.12 C +ATOM 50 CD LYS A 6 24.348 39.296 14.642 1.00 14.54 C +ATOM 51 CE LYS A 6 23.865 40.723 14.749 1.00 18.84 C +ATOM 52 NZ LYS A 6 22.375 40.720 14.907 1.00 20.55 N +ATOM 53 N THR A 7 29.426 38.430 15.446 1.00 7.41 N +ATOM 54 CA THR A 7 30.225 38.643 16.662 1.00 7.48 C +ATOM 55 C THR A 7 29.664 39.839 17.434 1.00 8.75 C +ATOM 56 O THR A 7 28.850 40.565 16.859 1.00 8.58 O +ATOM 57 CB THR A 7 31.744 38.879 16.299 1.00 9.61 C +ATOM 58 OG1 THR A 7 31.737 40.257 15.824 1.00 11.78 O +ATOM 59 CG2 THR A 7 32.260 37.969 15.171 1.00 9.17 C +ATOM 60 N LEU A 8 30.132 40.069 18.642 1.00 9.84 N +ATOM 61 CA LEU A 8 29.607 41.180 19.467 1.00 14.15 C +ATOM 62 C LEU A 8 30.075 42.538 18.984 1.00 17.37 C +ATOM 63 O LEU A 8 29.586 43.570 19.483 1.00 17.01 O +ATOM 64 CB LEU A 8 29.919 40.890 20.938 1.00 16.63 C +ATOM 65 CG LEU A 8 29.183 39.722 21.581 1.00 18.88 C +ATOM 66 CD1 LEU A 8 29.308 39.750 23.095 1.00 19.31 C +ATOM 67 CD2 LEU A 8 27.700 39.721 21.228 1.00 18.59 C +ATOM 68 N THR A 9 30.991 42.571 17.998 1.00 18.33 N +ATOM 69 CA THR A 9 31.422 43.940 17.553 1.00 19.24 C +ATOM 70 C THR A 9 30.755 44.351 16.277 1.00 19.48 C +ATOM 71 O THR A 9 31.207 45.268 15.566 1.00 23.14 O +ATOM 72 CB THR A 9 32.979 43.918 17.445 1.00 18.97 C +ATOM 73 OG1 THR A 9 33.174 43.067 16.265 1.00 20.24 O +ATOM 74 CG2 THR A 9 33.657 43.319 18.672 1.00 19.70 C +ATOM 75 N GLY A 10 29.721 43.673 15.885 1.00 19.43 N +ATOM 76 CA GLY A 10 28.978 43.960 14.678 1.00 18.74 C +ATOM 77 C GLY A 10 29.604 43.507 13.393 1.00 17.62 C +ATOM 78 O GLY A 10 29.219 43.981 12.301 1.00 19.74 O +ATOM 79 N LYS A 11 30.563 42.623 13.495 1.00 13.56 N +ATOM 80 CA LYS A 11 31.191 42.012 12.331 1.00 11.91 C +ATOM 81 C LYS A 11 30.459 40.666 12.130 1.00 10.18 C +ATOM 82 O LYS A 11 30.253 39.991 13.133 1.00 9.10 O +ATOM 83 CB LYS A 11 32.672 41.717 12.505 1.00 13.43 C +ATOM 84 CG LYS A 11 33.280 41.086 11.227 1.00 16.69 C +ATOM 85 CD LYS A 11 34.762 40.799 11.470 1.00 17.92 C +ATOM 86 CE LYS A 11 35.614 40.847 10.240 1.00 20.81 C +ATOM 87 NZ LYS A 11 35.100 40.073 9.101 1.00 21.93 N +ATOM 88 N THR A 12 30.163 40.338 10.886 1.00 9.63 N +ATOM 89 CA THR A 12 29.542 39.020 10.653 1.00 9.85 C +ATOM 90 C THR A 12 30.494 38.261 9.729 1.00 11.66 C +ATOM 91 O THR A 12 30.849 38.850 8.706 1.00 12.33 O +ATOM 92 CB THR A 12 28.113 39.049 10.015 1.00 10.85 C +ATOM 93 OG1 THR A 12 27.280 39.722 10.996 1.00 10.91 O +ATOM 94 CG2 THR A 12 27.588 37.635 9.715 1.00 9.63 C +ATOM 95 N ILE A 13 30.795 37.015 10.095 1.00 10.42 N +ATOM 96 CA ILE A 13 31.720 36.289 9.176 1.00 11.84 C +ATOM 97 C ILE A 13 30.955 35.211 8.459 1.00 10.55 C +ATOM 98 O ILE A 13 30.025 34.618 9.040 1.00 11.92 O +ATOM 99 CB ILE A 13 32.995 35.883 9.934 1.00 14.86 C +ATOM 100 CG1 ILE A 13 33.306 34.381 9.840 1.00 14.87 C +ATOM 101 CG2 ILE A 13 33.109 36.381 11.435 1.00 17.08 C +ATOM 102 CD1 ILE A 13 34.535 34.028 10.720 1.00 16.46 C +ATOM 103 N THR A 14 31.244 34.986 7.197 1.00 9.39 N +ATOM 104 CA THR A 14 30.505 33.884 6.512 1.00 9.63 C +ATOM 105 C THR A 14 31.409 32.680 6.446 1.00 11.20 C +ATOM 106 O THR A 14 32.619 32.812 6.125 1.00 11.63 O +ATOM 107 CB THR A 14 30.091 34.393 5.078 1.00 10.38 C +ATOM 108 OG1 THR A 14 31.440 34.513 4.487 1.00 16.30 O +ATOM 109 CG2 THR A 14 29.420 35.756 5.119 1.00 11.66 C +ATOM 110 N LEU A 15 30.884 31.485 6.666 1.00 8.29 N +ATOM 111 CA LEU A 15 31.677 30.275 6.639 1.00 9.03 C +ATOM 112 C LEU A 15 31.022 29.288 5.665 1.00 8.59 C +ATOM 113 O LEU A 15 29.809 29.395 5.545 1.00 7.79 O +ATOM 114 CB LEU A 15 31.562 29.686 8.045 1.00 11.08 C +ATOM 115 CG LEU A 15 32.631 29.444 9.060 1.00 15.79 C +ATOM 116 CD1 LEU A 15 33.814 30.390 9.030 1.00 15.88 C +ATOM 117 CD2 LEU A 15 31.945 29.449 10.436 1.00 15.27 C +ATOM 118 N GLU A 16 31.834 28.412 5.125 1.00 11.04 N +ATOM 119 CA GLU A 16 31.220 27.341 4.275 1.00 11.50 C +ATOM 120 C GLU A 16 31.440 26.079 5.080 1.00 10.13 C +ATOM 121 O GLU A 16 32.576 25.802 5.461 1.00 9.83 O +ATOM 122 CB GLU A 16 31.827 27.262 2.894 1.00 17.22 C +ATOM 123 CG GLU A 16 31.363 28.410 1.962 1.00 23.33 C +ATOM 124 CD GLU A 16 31.671 28.291 0.498 1.00 26.99 C +ATOM 125 OE1 GLU A 16 30.869 28.621 -0.366 1.00 28.86 O +ATOM 126 OE2 GLU A 16 32.835 27.861 0.278 1.00 28.90 O +ATOM 127 N VAL A 17 30.310 25.458 5.384 1.00 8.99 N +ATOM 128 CA VAL A 17 30.288 24.245 6.193 1.00 8.85 C +ATOM 129 C VAL A 17 29.279 23.227 5.641 1.00 8.04 C +ATOM 130 O VAL A 17 28.478 23.522 4.725 1.00 8.99 O +ATOM 131 CB VAL A 17 29.903 24.590 7.665 1.00 9.78 C +ATOM 132 CG1 VAL A 17 30.862 25.496 8.389 1.00 12.05 C +ATOM 133 CG2 VAL A 17 28.476 25.135 7.705 1.00 10.54 C +ATOM 134 N GLU A 18 29.380 22.057 6.232 1.00 7.29 N +ATOM 135 CA GLU A 18 28.468 20.940 5.980 1.00 7.08 C +ATOM 136 C GLU A 18 27.819 20.609 7.316 1.00 6.45 C +ATOM 137 O GLU A 18 28.449 20.674 8.360 1.00 5.28 O +ATOM 138 CB GLU A 18 29.213 19.697 5.506 1.00 10.28 C +ATOM 139 CG GLU A 18 29.728 19.755 4.060 1.00 12.65 C +ATOM 140 CD GLU A 18 28.754 20.061 2.978 1.00 14.15 C +ATOM 141 OE1 GLU A 18 27.546 19.992 2.985 1.00 14.33 O +ATOM 142 OE2 GLU A 18 29.336 20.423 1.904 1.00 18.17 O +ATOM 143 N PRO A 19 26.559 20.220 7.288 1.00 7.24 N +ATOM 144 CA PRO A 19 25.829 19.825 8.494 1.00 7.07 C +ATOM 145 C PRO A 19 26.541 18.732 9.251 1.00 6.65 C +ATOM 146 O PRO A 19 26.333 18.536 10.457 1.00 6.37 O +ATOM 147 CB PRO A 19 24.469 19.332 7.952 1.00 7.61 C +ATOM 148 CG PRO A 19 24.299 20.134 6.704 1.00 8.16 C +ATOM 149 CD PRO A 19 25.714 20.108 6.073 1.00 7.49 C +ATOM 150 N SER A 20 27.361 17.959 8.559 1.00 6.80 N +ATOM 151 CA SER A 20 28.054 16.835 9.210 1.00 6.28 C +ATOM 152 C SER A 20 29.258 17.318 9.984 1.00 8.45 C +ATOM 153 O SER A 20 29.930 16.477 10.606 1.00 7.26 O +ATOM 154 CB SER A 20 28.523 15.820 8.182 1.00 8.57 C +ATOM 155 OG SER A 20 28.946 16.445 6.967 1.00 11.13 O +ATOM 156 N ASP A 21 29.599 18.599 9.828 1.00 7.50 N +ATOM 157 CA ASP A 21 30.796 19.083 10.566 1.00 7.70 C +ATOM 158 C ASP A 21 30.491 19.162 12.040 1.00 7.08 C +ATOM 159 O ASP A 21 29.367 19.523 12.441 1.00 8.11 O +ATOM 160 CB ASP A 21 31.155 20.515 10.048 1.00 11.00 C +ATOM 161 CG ASP A 21 31.923 20.436 8.755 1.00 15.32 C +ATOM 162 OD1 ASP A 21 32.493 19.374 8.456 1.00 18.03 O +ATOM 163 OD2 ASP A 21 31.838 21.402 7.968 1.00 14.36 O +ATOM 164 N THR A 22 31.510 18.936 12.852 1.00 5.37 N +ATOM 165 CA THR A 22 31.398 19.064 14.286 1.00 6.01 C +ATOM 166 C THR A 22 31.593 20.553 14.655 1.00 8.01 C +ATOM 167 O THR A 22 32.159 21.311 13.861 1.00 8.11 O +ATOM 168 CB THR A 22 32.492 18.193 14.995 1.00 8.92 C +ATOM 169 OG1 THR A 22 33.778 18.739 14.516 1.00 10.22 O +ATOM 170 CG2 THR A 22 32.352 16.700 14.630 1.00 9.65 C +ATOM 171 N ILE A 23 31.113 20.863 15.860 1.00 8.32 N +ATOM 172 CA ILE A 23 31.288 22.201 16.417 1.00 9.92 C +ATOM 173 C ILE A 23 32.776 22.519 16.577 1.00 10.01 C +ATOM 174 O ILE A 23 33.233 23.659 16.384 1.00 8.71 O +ATOM 175 CB ILE A 23 30.520 22.300 17.764 1.00 10.78 C +ATOM 176 CG1 ILE A 23 29.006 22.043 17.442 1.00 11.38 C +ATOM 177 CG2 ILE A 23 30.832 23.699 18.358 1.00 10.90 C +ATOM 178 CD1 ILE A 23 28.407 22.948 16.366 1.00 12.30 C +ATOM 179 N GLU A 24 33.548 21.526 16.950 1.00 9.54 N +ATOM 180 CA GLU A 24 35.031 21.722 17.069 1.00 11.81 C +ATOM 181 C GLU A 24 35.615 22.190 15.759 1.00 11.14 C +ATOM 182 O GLU A 24 36.532 23.046 15.724 1.00 10.62 O +ATOM 183 CB GLU A 24 35.667 20.383 17.447 1.00 19.24 C +ATOM 184 CG GLU A 24 37.128 20.293 17.872 1.00 27.76 C +ATOM 185 CD GLU A 24 37.561 18.851 18.082 1.00 32.92 C +ATOM 186 OE1 GLU A 24 37.758 18.024 17.195 1.00 34.80 O +ATOM 187 OE2 GLU A 24 37.628 18.599 19.313 1.00 36.51 O +ATOM 188 N ASN A 25 35.139 21.624 14.662 1.00 9.43 N +ATOM 189 CA ASN A 25 35.590 21.945 13.302 1.00 10.96 C +ATOM 190 C ASN A 25 35.238 23.382 12.920 1.00 9.68 C +ATOM 191 O ASN A 25 36.066 24.109 12.333 1.00 9.33 O +ATOM 192 CB ASN A 25 35.064 20.957 12.255 1.00 16.78 C +ATOM 193 CG ASN A 25 35.541 21.418 10.871 1.00 22.31 C +ATOM 194 OD1 ASN A 25 36.772 21.623 10.676 1.00 25.66 O +ATOM 195 ND2 ASN A 25 34.628 21.595 9.920 1.00 24.70 N +ATOM 196 N VAL A 26 34.007 23.745 13.250 1.00 6.52 N +ATOM 197 CA VAL A 26 33.533 25.097 12.978 1.00 5.53 C +ATOM 198 C VAL A 26 34.441 26.099 13.684 1.00 4.42 C +ATOM 199 O VAL A 26 34.883 27.090 13.093 1.00 3.40 O +ATOM 200 CB VAL A 26 32.060 25.257 13.364 1.00 3.86 C +ATOM 201 CG1 VAL A 26 31.684 26.749 13.342 1.00 7.25 C +ATOM 202 CG2 VAL A 26 31.152 24.421 12.477 1.00 8.12 C +ATOM 203 N LYS A 27 34.734 25.822 14.949 1.00 2.64 N +ATOM 204 CA LYS A 27 35.596 26.715 15.736 1.00 4.14 C +ATOM 205 C LYS A 27 36.975 26.826 15.107 1.00 5.58 C +ATOM 206 O LYS A 27 37.579 27.926 15.159 1.00 4.11 O +ATOM 207 CB LYS A 27 35.715 26.203 17.172 1.00 3.97 C +ATOM 208 CG LYS A 27 34.343 26.445 17.898 1.00 7.45 C +ATOM 209 CD LYS A 27 34.509 26.077 19.360 1.00 9.02 C +ATOM 210 CE LYS A 27 33.206 26.311 20.122 1.00 12.90 C +ATOM 211 NZ LYS A 27 33.455 25.910 21.546 1.00 15.47 N +ATOM 212 N ALA A 28 37.499 25.743 14.571 1.00 6.61 N +ATOM 213 CA ALA A 28 38.794 25.761 13.880 1.00 7.74 C +ATOM 214 C ALA A 28 38.728 26.591 12.611 1.00 9.17 C +ATOM 215 O ALA A 28 39.704 27.346 12.277 1.00 11.45 O +ATOM 216 CB ALA A 28 39.285 24.336 13.566 1.00 7.68 C +ATOM 217 N LYS A 29 37.633 26.543 11.867 1.00 8.96 N +ATOM 218 CA LYS A 29 37.471 27.391 10.668 1.00 7.90 C +ATOM 219 C LYS A 29 37.441 28.882 11.052 1.00 6.92 C +ATOM 220 O LYS A 29 38.020 29.772 10.382 1.00 6.87 O +ATOM 221 CB LYS A 29 36.193 27.058 9.911 1.00 10.28 C +ATOM 222 CG LYS A 29 36.153 25.620 9.409 1.00 14.94 C +ATOM 223 CD LYS A 29 34.758 25.280 8.900 1.00 19.69 C +ATOM 224 CE LYS A 29 34.793 24.264 7.767 1.00 22.63 C +ATOM 225 NZ LYS A 29 34.914 24.944 6.441 1.00 24.98 N +ATOM 226 N ILE A 30 36.811 29.170 12.192 1.00 4.57 N +ATOM 227 CA ILE A 30 36.731 30.570 12.645 1.00 5.58 C +ATOM 228 C ILE A 30 38.148 30.981 13.069 1.00 7.26 C +ATOM 229 O ILE A 30 38.544 32.150 12.856 1.00 9.46 O +ATOM 230 CB ILE A 30 35.708 30.776 13.806 1.00 5.36 C +ATOM 231 CG1 ILE A 30 34.228 30.630 13.319 1.00 2.94 C +ATOM 232 CG2 ILE A 30 35.874 32.138 14.512 1.00 2.78 C +ATOM 233 CD1 ILE A 30 33.284 30.504 14.552 1.00 2.00 C +ATOM 234 N GLN A 31 38.883 30.110 13.713 1.00 7.06 N +ATOM 235 CA GLN A 31 40.269 30.508 14.115 1.00 8.67 C +ATOM 236 C GLN A 31 41.092 30.808 12.851 1.00 10.90 C +ATOM 237 O GLN A 31 41.828 31.808 12.681 1.00 9.63 O +ATOM 238 CB GLN A 31 40.996 29.399 14.865 1.00 9.12 C +ATOM 239 CG GLN A 31 42.445 29.848 15.182 1.00 10.76 C +ATOM 240 CD GLN A 31 43.090 28.828 16.095 1.00 13.78 C +ATOM 241 OE1 GLN A 31 42.770 27.655 15.906 1.00 14.48 O +ATOM 242 NE2 GLN A 31 43.898 29.252 17.050 1.00 14.76 N +ATOM 243 N ASP A 32 41.001 29.878 11.931 1.00 10.93 N +ATOM 244 CA ASP A 32 41.718 30.022 10.643 1.00 14.01 C +ATOM 245 C ASP A 32 41.399 31.338 9.967 1.00 14.04 C +ATOM 246 O ASP A 32 42.260 32.036 9.381 1.00 13.39 O +ATOM 247 CB ASP A 32 41.398 28.780 9.810 1.00 18.01 C +ATOM 248 CG ASP A 32 42.626 28.557 8.928 1.00 24.33 C +ATOM 249 OD1 ASP A 32 43.666 28.262 9.539 1.00 26.29 O +ATOM 250 OD2 ASP A 32 42.430 28.812 7.728 1.00 25.17 O +ATOM 251 N LYS A 33 40.117 31.750 9.988 1.00 14.22 N +ATOM 252 CA LYS A 33 39.808 32.994 9.233 1.00 14.00 C +ATOM 253 C LYS A 33 39.837 34.271 9.995 1.00 12.37 C +ATOM 254 O LYS A 33 40.164 35.323 9.345 1.00 12.17 O +ATOM 255 CB LYS A 33 38.615 32.801 8.320 1.00 18.62 C +ATOM 256 CG LYS A 33 37.220 32.822 8.827 1.00 24.00 C +ATOM 257 CD LYS A 33 36.351 33.613 7.838 1.00 27.61 C +ATOM 258 CE LYS A 33 36.322 32.944 6.477 1.00 27.64 C +ATOM 259 NZ LYS A 33 35.768 33.945 5.489 1.00 30.06 N +ATOM 260 N GLU A 34 39.655 34.335 11.285 1.00 10.11 N +ATOM 261 CA GLU A 34 39.676 35.547 12.072 1.00 10.07 C +ATOM 262 C GLU A 34 40.675 35.527 13.200 1.00 9.32 C +ATOM 263 O GLU A 34 40.814 36.528 13.911 1.00 11.61 O +ATOM 264 CB GLU A 34 38.290 35.814 12.698 1.00 14.77 C +ATOM 265 CG GLU A 34 37.156 35.985 11.688 1.00 18.75 C +ATOM 266 CD GLU A 34 37.192 37.361 11.033 1.00 22.28 C +ATOM 267 OE1 GLU A 34 37.519 38.360 11.645 1.00 21.95 O +ATOM 268 OE2 GLU A 34 36.861 37.320 9.822 1.00 25.19 O +ATOM 269 N GLY A 35 41.317 34.393 13.432 1.00 7.22 N +ATOM 270 CA GLY A 35 42.345 34.269 14.431 1.00 6.29 C +ATOM 271 C GLY A 35 41.949 34.076 15.842 1.00 6.93 C +ATOM 272 O GLY A 35 42.829 34.000 16.739 1.00 7.41 O +ATOM 273 N ILE A 36 40.642 33.916 16.112 1.00 5.86 N +ATOM 274 CA ILE A 36 40.226 33.716 17.509 1.00 6.07 C +ATOM 275 C ILE A 36 40.449 32.278 17.945 1.00 6.36 C +ATOM 276 O ILE A 36 39.936 31.336 17.315 1.00 6.18 O +ATOM 277 CB ILE A 36 38.693 34.106 17.595 1.00 7.47 C +ATOM 278 CG1 ILE A 36 38.471 35.546 17.045 1.00 8.52 C +ATOM 279 CG2 ILE A 36 38.146 33.932 19.027 1.00 7.36 C +ATOM 280 CD1 ILE A 36 36.958 35.746 16.680 1.00 9.49 C +ATOM 281 N PRO A 37 41.189 32.085 19.031 1.00 8.65 N +ATOM 282 CA PRO A 37 41.461 30.751 19.594 1.00 9.18 C +ATOM 283 C PRO A 37 40.168 30.026 19.918 1.00 9.85 C +ATOM 284 O PRO A 37 39.264 30.662 20.521 1.00 8.51 O +ATOM 285 CB PRO A 37 42.195 31.142 20.913 1.00 11.42 C +ATOM 286 CG PRO A 37 42.904 32.414 20.553 1.00 9.27 C +ATOM 287 CD PRO A 37 41.822 33.188 19.813 1.00 8.33 C +ATOM 288 N PRO A 38 40.059 28.758 19.607 1.00 8.71 N +ATOM 289 CA PRO A 38 38.817 28.020 19.889 1.00 9.08 C +ATOM 290 C PRO A 38 38.421 28.048 21.341 1.00 9.28 C +ATOM 291 O PRO A 38 37.213 28.036 21.704 1.00 6.50 O +ATOM 292 CB PRO A 38 39.090 26.629 19.325 1.00 10.31 C +ATOM 293 CG PRO A 38 40.082 26.904 18.198 1.00 10.81 C +ATOM 294 CD PRO A 38 41.035 27.909 18.879 1.00 12.00 C +ATOM 295 N ASP A 39 39.374 28.090 22.240 1.00 11.20 N +ATOM 296 CA ASP A 39 39.063 28.063 23.695 1.00 14.96 C +ATOM 297 C ASP A 39 38.365 29.335 24.159 1.00 13.99 C +ATOM 298 O ASP A 39 37.684 29.390 25.221 1.00 13.75 O +ATOM 299 CB ASP A 39 40.340 27.692 24.468 1.00 24.16 C +ATOM 300 CG ASP A 39 40.559 28.585 25.675 1.00 31.06 C +ATOM 301 OD1 ASP A 39 40.716 29.809 25.456 1.00 35.55 O +ATOM 302 OD2 ASP A 39 40.549 28.090 26.840 1.00 34.22 O +ATOM 303 N GLN A 40 38.419 30.373 23.341 1.00 11.60 N +ATOM 304 CA GLN A 40 37.738 31.637 23.712 1.00 10.76 C +ATOM 305 C GLN A 40 36.334 31.742 23.087 1.00 8.01 C +ATOM 306 O GLN A 40 35.574 32.618 23.483 1.00 8.96 O +ATOM 307 CB GLN A 40 38.528 32.854 23.182 1.00 11.14 C +ATOM 308 CG GLN A 40 39.919 32.854 23.840 1.00 14.85 C +ATOM 309 CD GLN A 40 40.760 34.036 23.394 1.00 16.11 C +ATOM 310 OE1 GLN A 40 41.975 34.008 23.624 1.00 20.52 O +ATOM 311 NE2 GLN A 40 40.140 35.007 22.775 1.00 18.16 N +ATOM 312 N GLN A 41 36.000 30.860 22.172 1.00 6.52 N +ATOM 313 CA GLN A 41 34.738 30.875 21.473 1.00 3.87 C +ATOM 314 C GLN A 41 33.589 30.189 22.181 1.00 4.79 C +ATOM 315 O GLN A 41 33.580 29.009 22.499 1.00 6.34 O +ATOM 316 CB GLN A 41 34.876 30.237 20.066 1.00 4.20 C +ATOM 317 CG GLN A 41 36.012 30.860 19.221 1.00 3.20 C +ATOM 318 CD GLN A 41 36.083 30.194 17.875 1.00 4.89 C +ATOM 319 OE1 GLN A 41 35.048 29.702 17.393 1.00 5.21 O +ATOM 320 NE2 GLN A 41 37.228 30.126 17.233 1.00 7.13 N +ATOM 321 N ARG A 42 32.478 30.917 22.269 1.00 5.73 N +ATOM 322 CA ARG A 42 31.200 30.329 22.780 1.00 6.97 C +ATOM 323 C ARG A 42 30.210 30.509 21.650 1.00 7.15 C +ATOM 324 O ARG A 42 29.978 31.726 21.269 1.00 7.33 O +ATOM 325 CB ARG A 42 30.847 30.931 24.118 1.00 13.23 C +ATOM 326 CG ARG A 42 29.412 30.796 24.598 1.00 21.27 C +ATOM 327 CD ARG A 42 29.271 31.314 26.016 1.00 26.14 C +ATOM 328 NE ARG A 42 27.875 31.317 26.443 1.00 32.26 N +ATOM 329 CZ ARG A 42 27.132 32.423 26.574 1.00 34.32 C +ATOM 330 NH1 ARG A 42 27.630 33.656 26.461 1.00 35.30 N +ATOM 331 NH2 ARG A 42 25.810 32.299 26.732 1.00 36.39 N +ATOM 332 N LEU A 43 29.694 29.436 21.054 1.00 4.65 N +ATOM 333 CA LEU A 43 28.762 29.573 19.906 1.00 3.51 C +ATOM 334 C LEU A 43 27.331 29.317 20.364 1.00 5.56 C +ATOM 335 O LEU A 43 27.101 28.346 21.097 1.00 4.19 O +ATOM 336 CB LEU A 43 29.151 28.655 18.755 1.00 3.74 C +ATOM 337 CG LEU A 43 30.416 28.912 17.980 1.00 6.32 C +ATOM 338 CD1 LEU A 43 30.738 27.693 17.122 1.00 9.55 C +ATOM 339 CD2 LEU A 43 30.205 30.168 17.129 1.00 6.41 C +ATOM 340 N ILE A 44 26.436 30.232 20.004 1.00 4.58 N +ATOM 341 CA ILE A 44 25.034 30.170 20.401 1.00 5.55 C +ATOM 342 C ILE A 44 24.101 30.149 19.196 1.00 5.46 C +ATOM 343 O ILE A 44 24.196 30.948 18.287 1.00 6.04 O +ATOM 344 CB ILE A 44 24.639 31.426 21.286 1.00 6.80 C +ATOM 345 CG1 ILE A 44 25.646 31.670 22.421 1.00 10.31 C +ATOM 346 CG2 ILE A 44 23.181 31.309 21.824 1.00 7.39 C +ATOM 347 CD1 ILE A 44 25.778 30.436 23.356 1.00 13.90 C +ATOM 348 N PHE A 45 23.141 29.187 19.241 1.00 6.75 N +ATOM 349 CA PHE A 45 22.126 29.062 18.183 1.00 4.70 C +ATOM 350 C PHE A 45 20.835 28.629 18.904 1.00 6.34 C +ATOM 351 O PHE A 45 20.821 27.734 19.749 1.00 5.45 O +ATOM 352 CB PHE A 45 22.494 28.057 17.109 1.00 5.51 C +ATOM 353 CG PHE A 45 21.447 27.869 16.026 1.00 5.98 C +ATOM 354 CD1 PHE A 45 21.325 28.813 15.005 1.00 6.86 C +ATOM 355 CD2 PHE A 45 20.638 26.735 16.053 1.00 5.87 C +ATOM 356 CE1 PHE A 45 20.369 28.648 14.001 1.00 6.68 C +ATOM 357 CE2 PHE A 45 19.677 26.539 15.051 1.00 6.64 C +ATOM 358 CZ PHE A 45 19.593 27.465 14.021 1.00 6.84 C +ATOM 359 N ALA A 46 19.810 29.378 18.578 1.00 6.53 N +ATOM 360 CA ALA A 46 18.443 29.143 19.083 1.00 7.15 C +ATOM 361 C ALA A 46 18.453 28.941 20.591 1.00 9.00 C +ATOM 362 O ALA A 46 17.860 27.994 21.128 1.00 11.15 O +ATOM 363 CB ALA A 46 17.864 27.977 18.346 1.00 8.99 C +ATOM 364 N GLY A 47 19.172 29.808 21.243 1.00 9.35 N +ATOM 365 CA GLY A 47 19.399 29.894 22.655 1.00 11.68 C +ATOM 366 C GLY A 47 20.083 28.729 23.321 1.00 11.14 C +ATOM 367 O GLY A 47 19.991 28.584 24.561 1.00 13.93 O +ATOM 368 N LYS A 48 20.801 27.931 22.578 1.00 10.47 N +ATOM 369 CA LYS A 48 21.550 26.796 23.133 1.00 8.82 C +ATOM 370 C LYS A 48 23.046 27.087 22.913 1.00 7.68 C +ATOM 371 O LYS A 48 23.383 27.627 21.870 1.00 6.47 O +ATOM 372 CB LYS A 48 21.242 25.519 22.391 1.00 9.74 C +ATOM 373 CG LYS A 48 19.762 25.077 22.455 1.00 14.14 C +ATOM 374 CD LYS A 48 19.634 23.885 21.531 1.00 16.32 C +ATOM 375 CE LYS A 48 18.791 24.221 20.313 1.00 20.04 C +ATOM 376 NZ LYS A 48 17.440 24.655 20.827 1.00 23.92 N +ATOM 377 N GLN A 49 23.880 26.727 23.851 1.00 8.89 N +ATOM 378 CA GLN A 49 25.349 26.872 23.643 1.00 7.18 C +ATOM 379 C GLN A 49 25.743 25.586 22.922 1.00 8.23 C +ATOM 380 O GLN A 49 25.325 24.489 23.378 1.00 9.70 O +ATOM 381 CB GLN A 49 26.070 27.025 24.960 1.00 11.67 C +ATOM 382 CG GLN A 49 27.553 27.356 24.695 1.00 15.82 C +ATOM 383 CD GLN A 49 28.262 27.576 26.020 1.00 20.21 C +ATOM 384 OE1 GLN A 49 29.189 26.840 26.335 1.00 23.23 O +ATOM 385 NE2 GLN A 49 27.777 28.585 26.739 1.00 20.67 N +ATOM 386 N LEU A 50 26.465 25.689 21.833 1.00 6.51 N +ATOM 387 CA LEU A 50 26.826 24.521 21.012 1.00 7.41 C +ATOM 388 C LEU A 50 27.994 23.781 21.643 1.00 8.27 C +ATOM 389 O LEU A 50 28.904 24.444 22.098 1.00 8.34 O +ATOM 390 CB LEU A 50 27.043 24.992 19.571 1.00 7.13 C +ATOM 391 CG LEU A 50 25.931 25.844 18.959 1.00 7.53 C +ATOM 392 CD1 LEU A 50 26.203 26.083 17.471 1.00 8.14 C +ATOM 393 CD2 LEU A 50 24.577 25.190 19.079 1.00 9.11 C +ATOM 394 N GLU A 51 27.942 22.448 21.648 1.00 9.43 N +ATOM 395 CA GLU A 51 29.015 21.657 22.288 1.00 11.90 C +ATOM 396 C GLU A 51 29.942 21.106 21.240 1.00 11.49 C +ATOM 397 O GLU A 51 29.470 20.677 20.190 1.00 9.88 O +ATOM 398 CB GLU A 51 28.348 20.540 23.066 1.00 16.56 C +ATOM 399 CG GLU A 51 29.247 19.456 23.705 1.00 26.06 C +ATOM 400 CD GLU A 51 28.722 19.047 25.066 1.00 29.86 C +ATOM 401 OE1 GLU A 51 29.139 18.132 25.746 1.00 32.13 O +ATOM 402 OE2 GLU A 51 27.777 19.842 25.367 1.00 33.44 O +ATOM 403 N ASP A 52 31.233 21.090 21.459 1.00 12.71 N +ATOM 404 CA ASP A 52 32.262 20.670 20.514 1.00 16.56 C +ATOM 405 C ASP A 52 32.128 19.364 19.750 1.00 15.83 C +ATOM 406 O ASP A 52 32.546 19.317 18.558 1.00 17.21 O +ATOM 407 CB ASP A 52 33.638 20.716 21.242 1.00 21.05 C +ATOM 408 CG ASP A 52 34.174 22.129 21.354 1.00 25.12 C +ATOM 409 OD1 ASP A 52 35.252 22.322 21.958 1.00 28.37 O +ATOM 410 OD2 ASP A 52 33.544 23.086 20.883 1.00 25.82 O +ATOM 411 N GLY A 53 31.697 18.311 20.406 1.00 15.00 N +ATOM 412 CA GLY A 53 31.568 16.962 19.825 1.00 11.77 C +ATOM 413 C GLY A 53 30.320 16.698 19.051 1.00 11.10 C +ATOM 414 O GLY A 53 30.198 15.657 18.366 1.00 11.25 O +ATOM 415 N ARG A 54 29.340 17.594 19.076 1.00 8.53 N +ATOM 416 CA ARG A 54 28.108 17.439 18.276 1.00 9.05 C +ATOM 417 C ARG A 54 28.375 17.999 16.887 1.00 8.96 C +ATOM 418 O ARG A 54 29.326 18.786 16.690 1.00 11.60 O +ATOM 419 CB ARG A 54 26.926 18.191 18.892 1.00 7.97 C +ATOM 420 CG ARG A 54 26.621 17.799 20.352 1.00 9.62 C +ATOM 421 CD ARG A 54 26.010 16.370 20.280 1.00 12.20 C +ATOM 422 NE ARG A 54 26.975 15.521 20.942 1.00 18.23 N +ATOM 423 CZ ARG A 54 27.603 14.423 20.655 1.00 22.08 C +ATOM 424 NH1 ARG A 54 27.479 13.733 19.537 1.00 23.38 N +ATOM 425 NH2 ARG A 54 28.519 13.967 21.550 1.00 25.50 N +ATOM 426 N THR A 55 27.510 17.689 15.954 1.00 9.05 N +ATOM 427 CA THR A 55 27.574 18.192 14.563 1.00 9.03 C +ATOM 428 C THR A 55 26.482 19.280 14.432 1.00 8.15 C +ATOM 429 O THR A 55 25.609 19.388 15.287 1.00 5.91 O +ATOM 430 CB THR A 55 27.299 17.055 13.533 1.00 11.15 C +ATOM 431 OG1 THR A 55 25.925 16.611 13.913 1.00 11.95 O +ATOM 432 CG2 THR A 55 28.236 15.864 13.558 1.00 11.71 C +ATOM 433 N LEU A 56 26.585 20.063 13.378 1.00 6.91 N +ATOM 434 CA LEU A 56 25.594 21.109 13.072 1.00 8.29 C +ATOM 435 C LEU A 56 24.241 20.436 12.857 1.00 8.05 C +ATOM 436 O LEU A 56 23.264 20.951 13.329 1.00 10.17 O +ATOM 437 CB LEU A 56 26.084 21.888 11.833 1.00 6.60 C +ATOM 438 CG LEU A 56 27.426 22.616 11.902 1.00 7.73 C +ATOM 439 CD1 LEU A 56 27.718 23.341 10.578 1.00 9.85 C +ATOM 440 CD2 LEU A 56 27.380 23.721 12.955 1.00 8.64 C +ATOM 441 N SER A 57 24.240 19.233 12.246 1.00 8.92 N +ATOM 442 CA SER A 57 22.924 18.583 12.025 1.00 9.00 C +ATOM 443 C SER A 57 22.229 18.244 13.325 1.00 9.44 C +ATOM 444 O SER A 57 20.963 18.253 13.395 1.00 10.91 O +ATOM 445 CB SER A 57 23.059 17.326 11.154 1.00 10.32 C +ATOM 446 OG SER A 57 23.914 16.395 11.755 1.00 13.59 O +ATOM 447 N ASP A 58 22.997 17.978 14.366 1.00 9.11 N +ATOM 448 CA ASP A 58 22.418 17.638 15.693 1.00 7.91 C +ATOM 449 C ASP A 58 21.460 18.737 16.163 1.00 9.12 C +ATOM 450 O ASP A 58 20.497 18.506 16.900 1.00 8.61 O +ATOM 451 CB ASP A 58 23.461 17.331 16.741 1.00 8.41 C +ATOM 452 CG ASP A 58 24.184 16.016 16.619 1.00 11.50 C +ATOM 453 OD1 ASP A 58 25.303 15.894 17.152 1.00 10.05 O +ATOM 454 OD2 ASP A 58 23.572 15.107 15.975 1.00 11.70 O +ATOM 455 N TYR A 59 21.846 19.954 15.905 1.00 7.97 N +ATOM 456 CA TYR A 59 21.079 21.149 16.251 1.00 8.45 C +ATOM 457 C TYR A 59 20.142 21.590 15.149 1.00 10.98 C +ATOM 458 O TYR A 59 19.499 22.645 15.321 1.00 12.95 O +ATOM 459 CB TYR A 59 22.085 22.254 16.581 1.00 7.94 C +ATOM 460 CG TYR A 59 22.945 21.951 17.785 1.00 6.91 C +ATOM 461 CD1 TYR A 59 24.272 21.544 17.644 1.00 4.59 C +ATOM 462 CD2 TYR A 59 22.437 22.157 19.065 1.00 6.98 C +ATOM 463 CE1 TYR A 59 25.052 21.285 18.776 1.00 5.39 C +ATOM 464 CE2 TYR A 59 23.204 21.907 20.192 1.00 6.52 C +ATOM 465 CZ TYR A 59 24.517 21.470 20.030 1.00 6.76 C +ATOM 466 OH TYR A 59 25.248 21.302 21.191 1.00 7.63 O +ATOM 467 N ASN A 60 19.993 20.884 14.049 1.00 12.38 N +ATOM 468 CA ASN A 60 19.065 21.352 12.999 1.00 13.94 C +ATOM 469 C ASN A 60 19.442 22.745 12.510 1.00 14.16 C +ATOM 470 O ASN A 60 18.571 23.610 12.289 1.00 14.26 O +ATOM 471 CB ASN A 60 17.586 21.282 13.461 1.00 19.23 C +ATOM 472 CG ASN A 60 16.576 21.258 12.315 1.00 22.65 C +ATOM 473 OD1 ASN A 60 15.440 21.819 12.378 1.00 25.45 O +ATOM 474 ND2 ASN A 60 16.924 20.586 11.216 1.00 24.09 N +ATOM 475 N ILE A 61 20.717 22.964 12.260 1.00 11.08 N +ATOM 476 CA ILE A 61 21.184 24.263 11.690 1.00 11.78 C +ATOM 477 C ILE A 61 21.110 24.111 10.173 1.00 13.74 C +ATOM 478 O ILE A 61 21.841 23.198 9.686 1.00 14.60 O +ATOM 479 CB ILE A 61 22.650 24.516 12.172 1.00 11.80 C +ATOM 480 CG1 ILE A 61 22.662 24.819 13.699 1.00 11.56 C +ATOM 481 CG2 ILE A 61 23.376 25.645 11.409 1.00 13.29 C +ATOM 482 CD1 ILE A 61 24.123 24.981 14.195 1.00 11.42 C +ATOM 483 N GLN A 62 20.291 24.875 9.507 1.00 13.97 N +ATOM 484 CA GLN A 62 20.081 24.773 8.033 1.00 15.52 C +ATOM 485 C GLN A 62 20.822 25.914 7.332 1.00 13.94 C +ATOM 486 O GLN A 62 21.323 26.830 8.008 1.00 12.15 O +ATOM 487 CB GLN A 62 18.599 24.736 7.727 1.00 19.53 C +ATOM 488 CG GLN A 62 17.819 23.434 7.900 1.00 26.38 C +ATOM 489 CD GLN A 62 16.509 23.529 7.116 1.00 30.61 C +ATOM 490 OE1 GLN A 62 15.446 22.980 7.433 1.00 33.23 O +ATOM 491 NE2 GLN A 62 16.539 24.293 6.009 1.00 32.71 N +ATOM 492 N LYS A 63 20.924 25.862 6.006 1.00 11.73 N +ATOM 493 CA LYS A 63 21.656 26.847 5.240 1.00 11.97 C +ATOM 494 C LYS A 63 21.127 28.240 5.574 1.00 10.41 C +ATOM 495 O LYS A 63 19.958 28.465 5.842 1.00 9.59 O +ATOM 496 CB LYS A 63 21.631 26.642 3.731 1.00 13.73 C +ATOM 497 CG LYS A 63 20.210 26.423 3.175 1.00 16.98 C +ATOM 498 CD LYS A 63 20.268 26.589 1.656 1.00 20.19 C +ATOM 499 CE LYS A 63 19.202 25.857 0.891 1.00 23.42 C +ATOM 500 NZ LYS A 63 17.884 26.544 1.075 1.00 25.97 N +ATOM 501 N GLU A 64 22.099 29.163 5.605 1.00 10.04 N +ATOM 502 CA GLU A 64 21.907 30.563 5.881 1.00 10.94 C +ATOM 503 C GLU A 64 21.466 30.953 7.261 1.00 9.74 C +ATOM 504 O GLU A 64 21.066 32.112 7.533 1.00 9.42 O +ATOM 505 CB GLU A 64 21.023 31.223 4.784 1.00 18.31 C +ATOM 506 CG GLU A 64 21.861 31.342 3.474 1.00 24.16 C +ATOM 507 CD GLU A 64 21.156 30.726 2.311 1.00 29.00 C +ATOM 508 OE1 GLU A 64 19.942 30.793 2.170 1.00 31.72 O +ATOM 509 OE2 GLU A 64 21.954 30.152 1.535 1.00 32.61 O +ATOM 510 N SER A 65 21.674 30.034 8.191 1.00 6.85 N +ATOM 511 CA SER A 65 21.419 30.253 9.620 1.00 6.90 C +ATOM 512 C SER A 65 22.504 31.228 10.136 1.00 4.72 C +ATOM 513 O SER A 65 23.579 31.321 9.554 1.00 3.91 O +ATOM 514 CB SER A 65 21.637 28.923 10.353 1.00 7.28 C +ATOM 515 OG SER A 65 20.544 28.047 10.059 1.00 10.56 O +ATOM 516 N THR A 66 22.241 31.873 11.241 1.00 4.48 N +ATOM 517 CA THR A 66 23.212 32.762 11.891 1.00 3.80 C +ATOM 518 C THR A 66 23.509 32.224 13.290 1.00 4.60 C +ATOM 519 O THR A 66 22.544 31.942 14.034 1.00 5.33 O +ATOM 520 CB THR A 66 22.699 34.267 11.985 1.00 2.85 C +ATOM 521 OG1 THR A 66 22.495 34.690 10.589 1.00 2.15 O +ATOM 522 CG2 THR A 66 23.727 35.131 12.722 1.00 3.40 C +ATOM 523 N LEU A 67 24.790 32.021 13.618 1.00 4.17 N +ATOM 524 CA LEU A 67 25.149 31.609 14.980 1.00 3.85 C +ATOM 525 C LEU A 67 25.698 32.876 15.669 1.00 3.80 C +ATOM 526 O LEU A 67 26.158 33.730 14.894 1.00 5.54 O +ATOM 527 CB LEU A 67 26.310 30.594 14.967 1.00 7.18 C +ATOM 528 CG LEU A 67 26.290 29.480 13.960 1.00 9.67 C +ATOM 529 CD1 LEU A 67 27.393 28.442 14.229 1.00 8.12 C +ATOM 530 CD2 LEU A 67 24.942 28.807 13.952 1.00 11.66 C +ATOM 531 N HIS A 68 25.621 32.945 16.950 1.00 2.94 N +ATOM 532 CA HIS A 68 26.179 34.127 17.650 1.00 4.17 C +ATOM 533 C HIS A 68 27.475 33.651 18.304 1.00 5.32 C +ATOM 534 O HIS A 68 27.507 32.587 18.958 1.00 7.70 O +ATOM 535 CB HIS A 68 25.214 34.565 18.780 1.00 5.57 C +ATOM 536 CG HIS A 68 23.978 35.121 18.126 1.00 9.95 C +ATOM 537 ND1 HIS A 68 23.853 36.432 17.781 1.00 13.74 N +ATOM 538 CD2 HIS A 68 22.824 34.514 17.782 1.00 12.79 C +ATOM 539 CE1 HIS A 68 22.674 36.627 17.200 1.00 14.75 C +ATOM 540 NE2 HIS A 68 22.045 35.455 17.173 1.00 16.30 N +ATOM 541 N LEU A 69 28.525 34.447 18.189 1.00 5.29 N +ATOM 542 CA LEU A 69 29.801 34.145 18.829 1.00 3.97 C +ATOM 543 C LEU A 69 30.052 35.042 20.004 1.00 5.07 C +ATOM 544 O LEU A 69 30.105 36.305 19.788 1.00 4.34 O +ATOM 545 CB LEU A 69 30.925 34.304 17.753 1.00 6.08 C +ATOM 546 CG LEU A 69 32.345 34.183 18.358 1.00 7.37 C +ATOM 547 CD1 LEU A 69 32.555 32.783 18.870 1.00 6.87 C +ATOM 548 CD2 LEU A 69 33.361 34.491 17.245 1.00 9.96 C +ATOM 549 N VAL A 70 30.124 34.533 21.191 1.00 4.29 N +ATOM 550 CA VAL A 70 30.479 35.369 22.374 1.00 6.26 C +ATOM 551 C VAL A 70 31.901 34.910 22.728 1.00 9.22 C +ATOM 552 O VAL A 70 32.190 33.696 22.635 1.00 9.36 O +ATOM 553 CB VAL A 70 29.472 35.181 23.498 1.00 8.69 C +ATOM 554 CG1 VAL A 70 29.821 35.957 24.765 1.00 9.76 C +ATOM 555 CG2 VAL A 70 28.049 35.454 23.071 1.00 8.54 C +ATOM 556 N LEU A 71 32.763 35.831 23.090 1.00 12.71 N +ATOM 557 CA LEU A 71 34.145 35.472 23.481 1.00 16.06 C +ATOM 558 C LEU A 71 34.239 35.353 24.979 1.00 18.09 C +ATOM 559 O LEU A 71 33.707 36.197 25.728 1.00 19.26 O +ATOM 560 CB LEU A 71 35.114 36.564 22.907 1.00 17.10 C +ATOM 561 CG LEU A 71 35.926 35.979 21.737 1.00 19.37 C +ATOM 562 CD1 LEU A 71 35.003 35.084 20.920 1.00 17.51 C +ATOM 563 CD2 LEU A 71 36.533 37.087 20.917 1.00 19.57 C +ATOM 564 N ARG A 72 34.930 34.384 25.451 1.00 21.47 N +ATOM 565 CA ARG A 72 35.161 34.174 26.896 1.00 25.83 C +ATOM 566 C ARG A 72 36.671 34.296 27.089 1.00 27.74 C +ATOM 567 O ARG A 72 37.305 33.233 26.795 1.00 30.65 O +ATOM 568 CB ARG A 72 34.717 32.760 27.286 1.00 28.49 C +ATOM 569 CG ARG A 72 35.752 32.054 28.160 1.00 31.79 C +ATOM 570 CD ARG A 72 35.612 30.577 28.044 1.00 34.05 C +ATOM 571 NE ARG A 72 35.040 30.252 26.730 1.00 35.08 N +ATOM 572 CZ ARG A 72 34.338 29.103 26.650 1.00 34.67 C +ATOM 573 NH1 ARG A 72 34.110 28.437 27.768 1.00 35.02 N +ATOM 574 NH2 ARG A 72 34.014 28.657 25.457 1.00 34.97 N +ATOM 575 N LEU A 73 37.197 35.397 27.513 0.45 28.93 N +ATOM 576 CA LEU A 73 38.668 35.502 27.680 0.45 30.76 C +ATOM 577 C LEU A 73 39.076 34.931 29.031 0.45 32.18 C +ATOM 578 O LEU A 73 38.297 34.946 29.996 0.45 32.31 O +ATOM 579 CB LEU A 73 39.080 36.941 27.406 0.45 30.53 C +ATOM 580 CG LEU A 73 39.502 37.340 26.002 0.45 30.16 C +ATOM 581 CD1 LEU A 73 38.684 36.647 24.923 0.45 29.57 C +ATOM 582 CD2 LEU A 73 39.337 38.854 25.862 0.45 29.11 C +ATOM 583 N ARG A 74 40.294 34.412 29.045 0.45 33.82 N +ATOM 584 CA ARG A 74 40.873 33.802 30.253 0.45 35.33 C +ATOM 585 C ARG A 74 41.765 34.829 30.944 0.45 36.22 C +ATOM 586 O ARG A 74 42.945 34.994 30.583 0.45 36.70 O +ATOM 587 CB ARG A 74 41.651 32.529 29.923 0.45 36.91 C +ATOM 588 CG ARG A 74 41.608 31.444 30.989 0.45 38.62 C +ATOM 589 CD ARG A 74 41.896 30.080 30.456 0.45 39.75 C +ATOM 590 NE ARG A 74 43.311 29.735 30.563 0.45 41.13 N +ATOM 591 CZ ARG A 74 44.174 29.905 29.554 0.45 41.91 C +ATOM 592 NH1 ARG A 74 43.754 30.312 28.356 0.45 42.75 N +ATOM 593 NH2 ARG A 74 45.477 29.726 29.763 0.45 41.93 N +ATOM 594 N GLY A 75 41.165 35.531 31.898 0.25 36.31 N +ATOM 595 CA GLY A 75 41.845 36.550 32.686 0.25 36.07 C +ATOM 596 C GLY A 75 41.251 37.941 32.588 0.25 36.16 C +ATOM 597 O GLY A 75 41.102 38.523 31.500 0.25 36.26 O +ATOM 598 N GLY A 76 40.946 38.472 33.757 0.25 36.05 N +ATOM 599 CA GLY A 76 40.373 39.813 33.944 0.25 36.19 C +ATOM 600 C GLY A 76 40.031 39.992 35.432 0.25 36.20 C +ATOM 601 O GLY A 76 38.933 40.525 35.687 0.25 36.13 O +ATOM 602 OXT GLY A 76 40.862 39.575 36.251 0.25 36.27 O +TER 603 GLY A 76 +HETATM 604 O HOH A 77 45.747 30.081 19.708 1.00 12.43 O +HETATM 605 O HOH A 78 19.168 31.868 17.050 1.00 12.65 O +HETATM 606 O HOH A 79 32.010 38.387 19.636 1.00 12.83 O +HETATM 607 O HOH A 80 42.084 27.361 21.953 1.00 22.27 O +HETATM 608 O HOH A 81 21.314 20.644 8.719 1.00 18.33 O +HETATM 609 O HOH A 82 31.965 38.637 3.699 1.00 31.69 O +HETATM 610 O HOH A 83 27.707 15.908 4.653 1.00 20.30 O +HETATM 611 O HOH A 84 19.969 32.720 14.769 1.00 10.14 O +HETATM 612 O HOH A 85 29.847 13.577 10.864 1.00 29.65 O +HETATM 613 O HOH A 86 23.893 27.864 1.501 1.00 23.48 O +HETATM 614 O HOH A 87 19.638 23.312 4.775 1.00 18.40 O +HETATM 615 O HOH A 88 34.628 29.369 4.779 1.00 26.17 O +HETATM 616 O HOH A 89 42.240 24.744 25.707 1.00 31.34 O +HETATM 617 O HOH A 90 30.290 42.500 8.820 1.00 16.49 O +HETATM 618 O HOH A 91 24.512 39.162 10.841 1.00 13.14 O +HETATM 619 O HOH A 92 26.557 43.450 19.940 1.00 19.38 O +HETATM 620 O HOH A 93 42.535 22.385 13.872 1.00 29.35 O +HETATM 621 O HOH A 94 42.440 26.381 12.686 1.00 29.46 O +HETATM 622 O HOH A 95 22.651 14.457 13.085 1.00 22.07 O +HETATM 623 O HOH A 96 35.325 26.551 23.202 1.00 15.20 O +HETATM 624 O HOH A 97 23.629 20.940 3.146 1.00 15.45 O +HETATM 625 O HOH A 98 25.928 21.774 2.325 1.00 13.70 O +HETATM 626 O HOH A 99 33.388 21.973 5.659 1.00 24.89 O +HETATM 627 O HOH A 100 18.326 23.911 17.697 1.00 24.10 O +HETATM 628 O HOH A 101 18.160 27.072 10.662 1.00 20.76 O +HETATM 629 O HOH A 102 34.746 17.167 18.219 1.00 32.86 O +HETATM 630 O HOH A 103 19.801 32.364 20.210 1.00 21.09 O +HETATM 631 O HOH A 104 30.285 26.829 22.191 1.00 8.56 O +HETATM 632 O HOH A 105 44.612 32.306 16.961 1.00 7.69 O +HETATM 633 O HOH A 106 16.287 25.999 13.142 0.78 28.90 O +HETATM 634 O HOH A 107 27.101 42.135 15.494 0.51 23.36 O +HETATM 635 O HOH A 108 37.209 23.795 21.367 0.74 27.88 O +HETATM 636 O HOH A 109 19.582 32.034 -0.685 0.49 22.24 O +HETATM 637 O HOH A 110 28.824 25.094 0.886 0.77 36.99 O +HETATM 638 O HOH A 111 25.146 19.162 25.323 0.87 36.70 O +HETATM 639 O HOH A 112 20.747 37.769 14.674 0.85 29.64 O +HETATM 640 O HOH A 113 16.035 17.841 8.765 0.61 23.89 O +HETATM 641 O HOH A 114 35.712 46.814 12.926 0.48 27.11 O +HETATM 642 O HOH A 115 15.570 27.475 7.482 0.51 24.18 O +HETATM 643 O HOH A 116 33.447 21.075 2.918 0.59 26.03 O +HETATM 644 O HOH A 117 41.116 39.021 13.061 0.63 22.39 O +HETATM 645 O HOH A 118 32.346 13.689 18.912 0.48 24.09 O +HETATM 646 O HOH A 119 31.197 13.048 7.920 0.71 29.54 O +HETATM 647 O HOH A 120 42.853 39.375 29.308 0.64 46.90 O +HETATM 648 O HOH A 121 39.646 23.959 9.699 0.41 18.25 O +HETATM 649 O HOH A 122 34.405 45.181 13.420 0.87 26.13 O +HETATM 650 O HOH A 123 26.517 24.300 27.592 0.41 21.02 O +HETATM 651 O HOH A 124 40.740 38.734 9.602 0.45 16.60 O +HETATM 652 O HOH A 125 31.494 18.276 23.170 0.67 26.53 O +HETATM 653 O HOH A 126 37.752 30.947 1.059 0.87 32.52 O +HETATM 654 O HOH A 127 31.771 16.941 7.511 0.64 15.94 O +HETATM 655 O HOH A 128 41.628 24.537 10.145 0.57 22.53 O +HETATM 656 O HOH A 129 28.988 22.175 -1.744 0.56 29.32 O +HETATM 657 O HOH A 130 14.882 16.539 10.692 0.53 24.82 O +HETATM 658 O HOH A 131 32.589 40.385 7.523 0.36 26.01 O +HETATM 659 O HOH A 132 38.363 30.369 5.579 0.49 35.45 O +HETATM 660 O HOH A 133 27.841 46.062 17.589 0.81 32.15 O +HETATM 661 O HOH A 134 37.667 43.421 17.000 0.50 33.32 O +MASTER 274 0 0 2 5 0 0 6 660 1 0 6 +END diff --git a/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/cg.pdb b/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/cg.pdb new file mode 100644 index 000000000..21cd29ce4 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/cg.pdb @@ -0,0 +1,263 @@ +ATOM 1 BB MET A 1 27.168 25.742 3.357 1.00 0.00 +ATOM 2 SC1 MET A 1 24.481 24.285 5.673 1.00 0.00 +ATOM 3 BB GLN A 2 25.962 28.749 4.446 1.00 0.00 +ATOM 4 SC1 GLN A 2 26.776 32.120 2.397 1.00 0.00 +ATOM 5 BB ILE A 3 27.033 30.748 7.177 1.00 0.00 +ATOM 6 SC1 ILE A 3 26.903 28.414 9.087 1.00 0.00 +ATOM 7 BB PHE A 4 26.587 32.877 10.061 1.00 0.00 +ATOM 8 SC1 PHE A 4 25.404 34.579 7.877 1.00 0.00 +ATOM 9 SC2 PHE A 4 24.102 34.183 5.906 1.00 0.00 +ATOM 10 SC3 PHE A 4 25.636 35.236 5.594 1.00 0.00 +ATOM 11 BB VAL A 5 28.795 34.925 12.172 1.00 0.00 +ATOM 12 SC1 VAL A 5 30.044 32.850 13.157 1.00 0.00 +ATOM 13 BB LYS A 6 28.034 36.809 14.994 1.00 0.00 +ATOM 14 SC1 LYS A 6 25.484 38.706 14.521 1.00 0.00 +ATOM 15 SC2 LYS A 6 23.063 40.721 14.834 1.00 0.00 +ATOM 16 BB THR A 7 29.486 39.423 16.577 1.00 0.00 +ATOM 17 SC1 THR A 7 31.896 39.157 15.771 1.00 0.00 +ATOM 18 BB LEU A 8 29.841 41.902 19.151 1.00 0.00 +ATOM 19 SC1 LEU A 8 29.027 40.021 21.711 1.00 0.00 +ATOM 20 BB THR A 9 31.098 44.070 16.796 1.00 0.00 +ATOM 21 SC1 THR A 9 33.260 43.398 17.341 1.00 0.00 +ATOM 22 BB GLY A 10 29.381 43.791 14.001 1.00 0.00 +ATOM 23 BB LYS A 11 30.588 41.272 12.826 1.00 0.00 +ATOM 24 SC1 LYS A 11 33.571 41.201 11.734 1.00 0.00 +ATOM 25 SC2 LYS A 11 35.337 40.430 9.627 1.00 0.00 +ATOM 26 BB THR A 12 30.302 39.143 9.931 1.00 0.00 +ATOM 27 SC1 THR A 12 27.622 38.894 10.317 1.00 0.00 +ATOM 28 BB ILE A 13 30.808 35.743 9.215 1.00 0.00 +ATOM 29 SC1 ILE A 13 33.486 35.168 10.482 1.00 0.00 +ATOM 30 BB THR A 14 31.524 33.585 6.560 1.00 0.00 +ATOM 31 SC1 THR A 14 30.429 34.850 4.854 1.00 0.00 +ATOM 32 BB LEU A 15 30.772 30.109 6.105 1.00 0.00 +ATOM 33 SC1 LEU A 15 32.488 29.742 9.143 1.00 0.00 +ATOM 34 BB GLU A 16 31.830 26.882 5.026 1.00 0.00 +ATOM 35 SC1 GLU A 16 31.729 28.107 0.924 1.00 0.00 +ATOM 36 BB VAL A 17 29.533 24.119 5.426 1.00 0.00 +ATOM 37 SC1 VAL A 17 29.747 25.074 7.920 1.00 0.00 +ATOM 38 BB GLU A 18 28.555 21.077 7.047 1.00 0.00 +ATOM 39 SC1 GLU A 18 28.860 20.012 3.364 1.00 0.00 +ATOM 40 BB PRO A 19 26.326 19.303 8.931 1.00 0.00 +ATOM 41 SC1 PRO A 19 24.827 19.858 6.910 1.00 0.00 +ATOM 42 BB SER A 20 28.698 17.128 9.627 1.00 0.00 +ATOM 43 SC1 SER A 20 28.765 16.177 7.488 1.00 0.00 +ATOM 44 BB ASP A 21 29.994 19.105 11.258 1.00 0.00 +ATOM 45 SC1 ASP A 21 31.897 20.425 8.722 1.00 0.00 +ATOM 46 BB THR A 22 31.696 20.027 13.870 1.00 0.00 +ATOM 47 SC1 THR A 22 32.964 17.964 14.694 1.00 0.00 +ATOM 48 BB ILE A 23 32.150 22.357 16.298 1.00 0.00 +ATOM 49 SC1 ILE A 23 29.691 22.748 17.483 1.00 0.00 +ATOM 50 BB GLU A 24 35.221 22.167 16.349 1.00 0.00 +ATOM 51 SC1 GLU A 24 37.212 19.122 18.014 1.00 0.00 +ATOM 52 BB ASN A 25 35.536 22.822 13.283 1.00 0.00 +ATOM 53 SC1 ASN A 25 35.563 21.422 10.874 1.00 0.00 +ATOM 54 BB VAL A 26 34.258 25.560 13.239 1.00 0.00 +ATOM 55 SC1 VAL A 26 31.632 25.476 13.061 1.00 0.00 +ATOM 56 BB LYS A 27 36.267 26.867 15.221 1.00 0.00 +ATOM 57 SC1 LYS A 27 34.856 26.242 18.143 1.00 0.00 +ATOM 58 SC2 LYS A 27 33.340 26.095 20.889 1.00 0.00 +ATOM 59 BB ALA A 28 38.713 26.410 13.302 1.00 0.00 +ATOM 60 SC1 ALA A 28 39.285 24.336 13.566 1.00 0.00 +ATOM 61 BB LYS A 29 37.669 28.208 10.979 1.00 0.00 +ATOM 62 SC1 LYS A 29 35.701 25.986 9.407 1.00 0.00 +ATOM 63 SC2 LYS A 29 34.858 24.630 7.053 1.00 0.00 +ATOM 64 BB ILE A 30 37.604 30.767 12.684 1.00 0.00 +ATOM 65 SC1 ILE A 30 34.773 31.012 14.047 1.00 0.00 +ATOM 66 BB GLN A 31 40.554 30.857 13.305 1.00 0.00 +ATOM 67 SC1 GLN A 31 42.686 28.923 15.862 1.00 0.00 +ATOM 68 BB ASP A 32 41.622 30.874 10.453 1.00 0.00 +ATOM 69 SC1 ASP A 32 42.604 28.593 8.949 1.00 0.00 +ATOM 70 BB LYS A 33 40.000 33.645 9.631 1.00 0.00 +ATOM 71 SC1 LYS A 33 37.395 33.079 8.328 1.00 0.00 +ATOM 72 SC2 LYS A 33 36.024 33.483 5.945 1.00 0.00 +ATOM 73 BB GLU A 34 40.230 35.519 12.664 1.00 0.00 +ATOM 74 SC1 GLU A 34 37.378 37.071 11.301 1.00 0.00 +ATOM 75 BB GLY A 35 42.134 34.179 15.169 1.00 0.00 +ATOM 76 BB ILE A 36 40.297 32.743 17.186 1.00 0.00 +ATOM 77 SC1 ILE A 36 38.067 34.832 17.587 1.00 0.00 +ATOM 78 BB PRO A 37 40.452 30.909 19.795 1.00 0.00 +ATOM 79 SC1 PRO A 37 42.307 32.248 20.426 1.00 0.00 +ATOM 80 BB PRO A 38 38.576 28.222 20.676 1.00 0.00 +ATOM 81 SC1 PRO A 38 40.069 27.147 18.801 1.00 0.00 +ATOM 82 BB ASP A 39 38.580 28.746 23.873 1.00 0.00 +ATOM 83 SC1 ASP A 39 40.554 28.602 25.687 1.00 0.00 +ATOM 84 BB GLN A 40 36.961 31.623 23.409 1.00 0.00 +ATOM 85 SC1 GLN A 40 40.364 33.805 23.361 1.00 0.00 +ATOM 86 BB GLN A 41 34.467 30.166 22.116 1.00 0.00 +ATOM 87 SC1 GLN A 41 35.843 30.189 18.265 1.00 0.00 +ATOM 88 BB ARG A 42 30.949 30.935 21.949 1.00 0.00 +ATOM 89 SC1 ARG A 42 29.843 31.014 24.911 1.00 0.00 +ATOM 90 SC2 ARG A 42 27.111 32.424 26.552 1.00 0.00 +ATOM 91 BB LEU A 43 28.193 29.117 20.658 1.00 0.00 +ATOM 92 SC1 LEU A 43 30.128 28.857 17.747 1.00 0.00 +ATOM 93 BB ILE A 44 24.942 30.412 19.404 1.00 0.00 +ATOM 94 SC1 ILE A 44 24.811 31.210 22.222 1.00 0.00 +ATOM 95 BB PHE A 45 21.716 28.605 19.082 1.00 0.00 +ATOM 96 SC1 PHE A 45 21.723 27.916 16.308 1.00 0.00 +ATOM 97 SC2 PHE A 45 20.484 28.426 14.315 1.00 0.00 +ATOM 98 SC3 PHE A 45 19.953 26.813 15.122 1.00 0.00 +ATOM 99 BB ALA A 46 18.627 28.819 19.893 1.00 0.00 +ATOM 100 SC1 ALA A 46 17.864 27.977 18.346 1.00 0.00 +ATOM 101 BB GLY A 47 19.668 29.225 23.002 1.00 0.00 +ATOM 102 BB LYS A 48 22.231 27.401 22.566 1.00 0.00 +ATOM 103 SC1 LYS A 48 20.213 24.827 22.126 1.00 0.00 +ATOM 104 SC2 LYS A 48 18.064 24.455 20.590 1.00 0.00 +ATOM 105 BB GLN A 49 25.049 25.843 23.458 1.00 0.00 +ATOM 106 SC1 GLN A 49 27.856 27.471 25.815 1.00 0.00 +ATOM 107 BB LEU A 50 27.608 24.637 21.687 1.00 0.00 +ATOM 108 SC1 LEU A 50 25.939 25.527 18.770 1.00 0.00 +ATOM 109 BB GLU A 51 29.078 21.449 21.268 1.00 0.00 +ATOM 110 SC1 GLU A 51 28.624 19.354 24.704 1.00 0.00 +ATOM 111 BB ASP A 52 32.050 20.088 20.010 1.00 0.00 +ATOM 112 SC1 ASP A 52 34.187 22.155 21.368 1.00 0.00 +ATOM 113 BB GLY A 53 30.918 16.866 19.371 1.00 0.00 +ATOM 114 BB ARG A 54 28.848 18.003 17.705 1.00 0.00 +ATOM 115 SC1 ARG A 54 26.519 17.453 19.841 1.00 0.00 +ATOM 116 SC2 ARG A 54 27.646 14.411 20.672 1.00 0.00 +ATOM 117 BB THR A 55 26.733 18.658 15.109 1.00 0.00 +ATOM 118 SC1 THR A 55 27.031 16.520 13.692 1.00 0.00 +ATOM 119 BB LEU A 56 24.860 20.641 13.180 1.00 0.00 +ATOM 120 SC1 LEU A 56 27.152 22.891 11.817 1.00 0.00 +ATOM 121 BB SER A 57 22.530 18.578 12.777 1.00 0.00 +ATOM 122 SC1 SER A 57 23.548 16.794 11.497 1.00 0.00 +ATOM 123 BB ASP A 58 21.786 18.228 15.811 1.00 0.00 +ATOM 124 SC1 ASP A 58 24.174 16.003 16.613 1.00 0.00 +ATOM 125 BB TYR A 59 20.601 21.380 15.641 1.00 0.00 +ATOM 126 SC1 TYR A 59 22.515 22.102 17.183 1.00 0.00 +ATOM 127 SC2 TYR A 59 24.662 21.414 18.210 1.00 0.00 +ATOM 128 SC3 TYR A 59 22.820 22.032 19.629 1.00 0.00 +ATOM 129 SC4 TYR A 59 24.935 21.374 20.693 1.00 0.00 +ATOM 130 BB ASN A 60 19.243 22.209 12.952 1.00 0.00 +ATOM 131 SC1 ASN A 60 16.554 21.255 12.303 1.00 0.00 +ATOM 132 BB ILE A 61 21.241 23.577 10.907 1.00 0.00 +ATOM 133 SC1 ILE A 61 23.203 24.990 12.869 1.00 0.00 +ATOM 134 BB GLN A 62 20.668 25.662 8.252 1.00 0.00 +ATOM 135 SC1 GLN A 62 16.876 23.760 7.212 1.00 0.00 +ATOM 136 BB LYS A 63 20.846 27.381 5.691 1.00 0.00 +ATOM 137 SC1 LYS A 63 20.703 26.551 2.854 1.00 0.00 +ATOM 138 SC2 LYS A 63 18.492 26.227 0.990 1.00 0.00 +ATOM 139 BB GLU A 64 21.610 30.746 6.606 1.00 0.00 +ATOM 140 SC1 GLU A 64 21.159 30.803 2.737 1.00 0.00 +ATOM 141 BB SER A 65 22.366 30.729 9.345 1.00 0.00 +ATOM 142 SC1 SER A 65 21.012 28.422 10.185 1.00 0.00 +ATOM 143 BB THR A 66 22.828 32.169 12.668 1.00 0.00 +ATOM 144 SC1 THR A 66 22.926 34.695 11.648 1.00 0.00 +ATOM 145 BB LEU A 67 25.477 32.626 14.755 1.00 0.00 +ATOM 146 SC1 LEU A 67 26.234 29.331 14.277 1.00 0.00 +ATOM 147 BB HIS A 68 26.716 33.258 18.001 1.00 0.00 +ATOM 148 SC1 HIS A 68 24.596 34.843 18.453 1.00 0.00 +ATOM 149 SC2 HIS A 68 22.405 35.021 17.454 1.00 0.00 +ATOM 150 SC3 HIS A 68 23.309 36.522 17.513 1.00 0.00 +ATOM 151 BB LEU A 69 29.616 35.063 19.208 1.00 0.00 +ATOM 152 SC1 LEU A 69 32.296 33.940 18.057 1.00 0.00 +ATOM 153 BB VAL A 70 31.210 34.555 22.223 1.00 0.00 +ATOM 154 SC1 VAL A 70 29.114 35.531 23.778 1.00 0.00 +ATOM 155 BB LEU A 71 33.678 35.753 24.378 1.00 0.00 +ATOM 156 SC1 LEU A 71 35.644 36.178 21.620 1.00 0.00 +ATOM 157 BB ARG A 72 36.072 33.977 26.534 1.00 0.00 +ATOM 158 SC1 ARG A 72 35.360 31.797 27.830 1.00 0.00 +ATOM 159 SC2 ARG A 72 34.377 29.113 26.651 1.00 0.00 +ATOM 160 BB LEU A 73 38.267 35.183 28.623 1.00 0.00 +ATOM 161 SC1 LEU A 73 39.151 37.446 26.048 1.00 0.00 +ATOM 162 BB ARG A 74 41.535 34.542 30.191 1.00 0.00 +ATOM 163 SC1 ARG A 74 41.718 31.351 30.456 1.00 0.00 +ATOM 164 SC2 ARG A 74 44.179 29.920 29.559 1.00 0.00 +ATOM 165 BB GLY A 75 41.317 37.180 32.109 1.00 0.00 +ATOM 166 BB GLY A 76 40.212 39.684 35.087 1.00 0.00 +TER 167 GLY A 76 +CONECT 1 2 3 +CONECT 3 4 5 +CONECT 5 6 7 +CONECT 7 8 11 +CONECT 8 9 10 +CONECT 9 10 +CONECT 11 12 13 +CONECT 13 14 16 +CONECT 14 15 +CONECT 16 17 18 +CONECT 18 19 20 +CONECT 20 21 22 +CONECT 22 23 +CONECT 23 24 26 +CONECT 24 25 +CONECT 26 27 28 +CONECT 28 29 30 +CONECT 30 31 32 +CONECT 32 33 34 +CONECT 34 35 36 +CONECT 36 37 38 +CONECT 38 39 40 +CONECT 40 41 42 +CONECT 42 43 44 +CONECT 44 45 46 +CONECT 46 47 48 +CONECT 48 49 50 +CONECT 50 51 52 +CONECT 52 53 54 +CONECT 54 55 56 +CONECT 56 57 59 +CONECT 57 58 +CONECT 59 60 61 +CONECT 61 62 64 +CONECT 62 63 +CONECT 64 65 66 +CONECT 66 67 68 +CONECT 68 69 70 +CONECT 70 71 73 +CONECT 71 72 +CONECT 73 74 75 +CONECT 75 76 +CONECT 76 77 78 +CONECT 78 79 80 +CONECT 80 81 82 +CONECT 82 83 84 +CONECT 84 85 86 +CONECT 86 87 88 +CONECT 88 89 91 +CONECT 89 90 +CONECT 91 92 93 +CONECT 93 94 95 +CONECT 95 96 99 +CONECT 96 97 98 +CONECT 97 98 +CONECT 99 100 101 +CONECT 101 102 +CONECT 102 103 105 +CONECT 103 104 +CONECT 105 106 107 +CONECT 107 108 109 +CONECT 109 110 111 +CONECT 111 112 113 +CONECT 113 114 +CONECT 114 115 117 +CONECT 115 116 +CONECT 117 118 119 +CONECT 119 120 121 +CONECT 121 122 123 +CONECT 123 124 125 +CONECT 125 126 130 +CONECT 126 127 128 +CONECT 127 128 129 +CONECT 128 129 +CONECT 130 131 132 +CONECT 132 133 134 +CONECT 134 135 136 +CONECT 136 137 139 +CONECT 137 138 +CONECT 139 140 141 +CONECT 141 142 143 +CONECT 143 144 145 +CONECT 145 146 147 +CONECT 147 148 151 +CONECT 148 149 150 +CONECT 149 150 +CONECT 151 152 153 +CONECT 153 154 155 +CONECT 155 156 157 +CONECT 157 158 160 +CONECT 158 159 +CONECT 160 161 162 +CONECT 162 163 165 +CONECT 163 164 +CONECT 165 166 +END \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/citation b/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/citation new file mode 100644 index 000000000..b61d3714e --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/citation @@ -0,0 +1,2 @@ +McGibbon, R T; Beauchamp, K A; Harrigan, M P; Klein, C; Swails, J M; Hernández, C X; Schwantes, C R; Wang, L; Lane, T J; Pande, V S; Biophysical Journal 2015; 10.1016/j.bpj.2015.08.015 +Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 diff --git a/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/command new file mode 100644 index 000000000..7d21335c4 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/command @@ -0,0 +1,8 @@ +martinize2 +-f ../aa.pdb +-ff martini3001 +-x cg.pdb +-o topol.top +-ignore HOH +-dssp +-elastic \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/molecule_0.itp b/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/molecule_0.itp new file mode 100644 index 000000000..a9ea6cf11 --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/molecule_0.itp @@ -0,0 +1,1112 @@ +; This file was generated using the following command: +; /coarse/chris/python_packages/vermouth_dev/vermouth-martinize/venv/bin/martinize2 -f aa.pdb -ff martini3001 -x cg.pdb -o topol.top -ignore HOH -dssp -elastic +; martinize with vermouth 0.0.1.dev1774 +; The following sequence of secondary structure +; was used for the full system: +; CEEEEEETTSCEEEEECCTTSBHHHHHHHHHHHHCCCGGGEEEEETTEECCTTSBTGGGTCCTTCEEEEEECCSCC + +; Please cite the following papers: +; McGibbon, R T; Beauchamp, K A; Harrigan, M P; Klein, C; Swails, J M; Hernández, C X; Schwantes, C R; Wang, L; Lane, T J; Pande, V S; Biophysical Journal 2015; 10.1016/j.bpj.2015.08.015 +; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 + +[ moleculetype ] +molecule_0 1 + +[ atoms ] + 1 Q5 1 MET BB 1 1 + 2 C6 1 MET SC1 2 0.0 + 3 P2 2 GLN BB 3 0.0 + 4 P5 2 GLN SC1 4 0.0 + 5 P2 3 ILE BB 5 0.0 + 6 SC2 3 ILE SC1 6 0.0 + 7 P2 4 PHE BB 7 0.0 + 8 SC4 4 PHE SC1 8 0.0 + 9 TC5 4 PHE SC2 9 0.0 + 10 TC5 4 PHE SC3 10 0.0 + 11 SP2 5 VAL BB 11 0.0 + 12 SC3 5 VAL SC1 12 0.0 + 13 P2 6 LYS BB 13 0.0 + 14 SC3 6 LYS SC1 14 0.0 + 15 SQ4p 6 LYS SC2 15 1.0 + 16 P2 7 THR BB 16 0.0 + 17 SP1 7 THR SC1 17 0.0 + 18 P2 8 LEU BB 18 0.0 + 19 SC2 8 LEU SC1 19 0.0 + 20 P2 9 THR BB 20 0.0 + 21 SP1 9 THR SC1 21 0.0 + 22 SP1 10 GLY BB 22 0.0 + 23 P2 11 LYS BB 23 0.0 + 24 SC3 11 LYS SC1 24 0.0 + 25 SQ4p 11 LYS SC2 25 1.0 + 26 P2 12 THR BB 26 0.0 + 27 SP1 12 THR SC1 27 0.0 + 28 P2 13 ILE BB 28 0.0 + 29 SC2 13 ILE SC1 29 0.0 + 30 P2 14 THR BB 30 0.0 + 31 SP1 14 THR SC1 31 0.0 + 32 P2 15 LEU BB 32 0.0 + 33 SC2 15 LEU SC1 33 0.0 + 34 P2 16 GLU BB 34 0.0 + 35 Q5n 16 GLU SC1 35 -1.0 + 36 SP2 17 VAL BB 36 0.0 + 37 SC3 17 VAL SC1 37 0.0 + 38 P2 18 GLU BB 38 0.0 + 39 Q5n 18 GLU SC1 39 -1.0 + 40 SP2a 19 PRO BB 40 0.0 + 41 SC3 19 PRO SC1 41 0.0 + 42 P2 20 SER BB 42 0.0 + 43 TP1 20 SER SC1 43 0.0 + 44 P2 21 ASP BB 44 0.0 + 45 SQ5n 21 ASP SC1 45 -1.0 + 46 P2 22 THR BB 46 0.0 + 47 SP1 22 THR SC1 47 0.0 + 48 P2 23 ILE BB 48 0.0 + 49 SC2 23 ILE SC1 49 0.0 + 50 P2 24 GLU BB 50 0.0 + 51 Q5n 24 GLU SC1 51 -1.0 + 52 P2 25 ASN BB 52 0.0 + 53 SP5 25 ASN SC1 53 0.0 + 54 SP2 26 VAL BB 54 0.0 + 55 SC3 26 VAL SC1 55 0.0 + 56 P2 27 LYS BB 56 0.0 + 57 SC3 27 LYS SC1 57 0.0 + 58 SQ4p 27 LYS SC2 58 1.0 + 59 SP2 28 ALA BB 59 0.0 + 60 TC3 28 ALA SC1 60 0.0 + 61 P2 29 LYS BB 61 0.0 + 62 SC3 29 LYS SC1 62 0.0 + 63 SQ4p 29 LYS SC2 63 1.0 + 64 P2 30 ILE BB 64 0.0 + 65 SC2 30 ILE SC1 65 0.0 + 66 P2 31 GLN BB 66 0.0 + 67 P5 31 GLN SC1 67 0.0 + 68 P2 32 ASP BB 68 0.0 + 69 SQ5n 32 ASP SC1 69 -1.0 + 70 P2 33 LYS BB 70 0.0 + 71 SC3 33 LYS SC1 71 0.0 + 72 SQ4p 33 LYS SC2 72 1.0 + 73 P2 34 GLU BB 73 0.0 + 74 Q5n 34 GLU SC1 74 -1.0 + 75 SP1 35 GLY BB 75 0.0 + 76 P2 36 ILE BB 76 0.0 + 77 SC2 36 ILE SC1 77 0.0 + 78 SP2a 37 PRO BB 78 0.0 + 79 SC3 37 PRO SC1 79 0.0 + 80 SP2a 38 PRO BB 80 0.0 + 81 SC3 38 PRO SC1 81 0.0 + 82 P2 39 ASP BB 82 0.0 + 83 SQ5n 39 ASP SC1 83 -1.0 + 84 P2 40 GLN BB 84 0.0 + 85 P5 40 GLN SC1 85 0.0 + 86 P2 41 GLN BB 86 0.0 + 87 P5 41 GLN SC1 87 0.0 + 88 P2 42 ARG BB 88 0.0 + 89 SC3 42 ARG SC1 89 0.0 + 90 SQ3p 42 ARG SC2 90 1.0 + 91 P2 43 LEU BB 91 0.0 + 92 SC2 43 LEU SC1 92 0.0 + 93 P2 44 ILE BB 93 0.0 + 94 SC2 44 ILE SC1 94 0.0 + 95 P2 45 PHE BB 95 0.0 + 96 SC4 45 PHE SC1 96 0.0 + 97 TC5 45 PHE SC2 97 0.0 + 98 TC5 45 PHE SC3 98 0.0 + 99 SP2 46 ALA BB 99 0.0 +100 TC3 46 ALA SC1 100 0.0 +101 SP1 47 GLY BB 101 0.0 +102 P2 48 LYS BB 102 0.0 +103 SC3 48 LYS SC1 103 0.0 +104 SQ4p 48 LYS SC2 104 1.0 +105 P2 49 GLN BB 105 0.0 +106 P5 49 GLN SC1 106 0.0 +107 P2 50 LEU BB 107 0.0 +108 SC2 50 LEU SC1 108 0.0 +109 P2 51 GLU BB 109 0.0 +110 Q5n 51 GLU SC1 110 -1.0 +111 P2 52 ASP BB 111 0.0 +112 SQ5n 52 ASP SC1 112 -1.0 +113 SP1 53 GLY BB 113 0.0 +114 P2 54 ARG BB 114 0.0 +115 SC3 54 ARG SC1 115 0.0 +116 SQ3p 54 ARG SC2 116 1.0 +117 P2 55 THR BB 117 0.0 +118 SP1 55 THR SC1 118 0.0 +119 P2 56 LEU BB 119 0.0 +120 SC2 56 LEU SC1 120 0.0 +121 P2 57 SER BB 121 0.0 +122 TP1 57 SER SC1 122 0.0 +123 P2 58 ASP BB 123 0.0 +124 SQ5n 58 ASP SC1 124 -1.0 +125 P2 59 TYR BB 125 0.0 +126 TC4 59 TYR SC1 126 0.0 +127 TC5 59 TYR SC2 127 0.0 +128 TC5 59 TYR SC3 128 0.0 +129 TN6 59 TYR SC4 129 0.0 +130 P2 60 ASN BB 130 0.0 +131 SP5 60 ASN SC1 131 0.0 +132 P2 61 ILE BB 132 0.0 +133 SC2 61 ILE SC1 133 0.0 +134 P2 62 GLN BB 134 0.0 +135 P5 62 GLN SC1 135 0.0 +136 P2 63 LYS BB 136 0.0 +137 SC3 63 LYS SC1 137 0.0 +138 SQ4p 63 LYS SC2 138 1.0 +139 P2 64 GLU BB 139 0.0 +140 Q5n 64 GLU SC1 140 -1.0 +141 P2 65 SER BB 141 0.0 +142 TP1 65 SER SC1 142 0.0 +143 P2 66 THR BB 143 0.0 +144 SP1 66 THR SC1 144 0.0 +145 P2 67 LEU BB 145 0.0 +146 SC2 67 LEU SC1 146 0.0 +147 P2 68 HIS BB 147 0.0 +148 TC4 68 HIS SC1 148 0.0 +149 TN6d 68 HIS SC2 149 0.0 +150 TN5a 68 HIS SC3 150 0.0 +151 P2 69 LEU BB 151 0.0 +152 SC2 69 LEU SC1 152 0.0 +153 SP2 70 VAL BB 153 0.0 +154 SC3 70 VAL SC1 154 0.0 +155 P2 71 LEU BB 155 0.0 +156 SC2 71 LEU SC1 156 0.0 +157 P2 72 ARG BB 157 0.0 +158 SC3 72 ARG SC1 158 0.0 +159 SQ3p 72 ARG SC2 159 1.0 +160 P2 73 LEU BB 160 0.0 +161 SC2 73 LEU SC1 161 0.0 +162 P2 74 ARG BB 162 0.0 +163 SC3 74 ARG SC1 163 0.0 +164 SQ3p 74 ARG SC2 164 1.0 +165 SP1 75 GLY BB 165 0.0 +166 Q5 76 GLY BB 166 -1 + +[ bonds ] +; Backbone bonds + 1 3 1 0.350 4000 + 3 5 1 0.350 4000 + 5 7 1 0.350 4000 + 7 11 1 0.350 4000 + 11 13 1 0.350 4000 + 13 16 1 0.350 4000 + 16 18 1 0.350 4000 + 18 20 1 0.350 4000 + 20 22 1 0.350 4000 + 22 23 1 0.350 4000 + 23 26 1 0.350 4000 + 26 28 1 0.350 4000 + 28 30 1 0.350 4000 + 30 32 1 0.350 4000 + 32 34 1 0.350 4000 + 34 36 1 0.350 4000 + 36 38 1 0.350 4000 + 38 40 1 0.350 4000 + 40 42 1 0.350 4000 + 42 44 1 0.350 4000 + 44 46 1 0.350 4000 + 75 76 1 0.350 4000 + 76 78 1 0.350 4000 + 86 88 1 0.350 4000 + 88 91 1 0.350 4000 + 91 93 1 0.350 4000 + 93 95 1 0.350 4000 + 95 99 1 0.350 4000 + 99 101 1 0.350 4000 +101 102 1 0.350 4000 +102 105 1 0.350 4000 +105 107 1 0.350 4000 +107 109 1 0.350 4000 +109 111 1 0.350 4000 +111 113 1 0.350 4000 +113 114 1 0.350 4000 +114 117 1 0.350 4000 +117 119 1 0.350 4000 +130 132 1 0.350 4000 +132 134 1 0.350 4000 +134 136 1 0.350 4000 +136 139 1 0.350 4000 +139 141 1 0.350 4000 +141 143 1 0.350 4000 +143 145 1 0.350 4000 +145 147 1 0.350 4000 +147 151 1 0.350 4000 +151 153 1 0.350 4000 +153 155 1 0.350 4000 +155 157 1 0.350 4000 +157 160 1 0.350 4000 +160 162 1 0.350 4000 +162 165 1 0.350 4000 +165 166 1 0.350 4000 + +; Long elastic bonds for extended regions + 3 11 1 0.970 2500 + 5 13 1 0.970 2500 + 7 16 1 0.970 2500 + 26 32 1 0.970 2500 + 28 34 1 0.970 2500 + 86 93 1 0.970 2500 + 88 95 1 0.970 2500 +143 151 1 0.970 2500 +145 153 1 0.970 2500 +147 155 1 0.970 2500 + +; Rubber band + 1 32 1 0.62939 700.0 + 1 34 1 0.50809 700.0 + 1 36 1 0.35363 700.0 + 1 38 1 0.61072 700.0 + 1 40 1 0.85582 700.0 + 1 134 1 0.81374 700.0 + 1 136 1 0.69362 700.0 + 1 139 1 0.81542 700.0 + 3 30 1 0.76674 700.0 + 3 32 1 0.52673 700.0 + 3 34 1 0.61852 700.0 + 3 36 1 0.5929 700.0 + 3 38 1 0.85057 700.0 + 3 134 1 0.72134 700.0 + 3 136 1 0.54404 700.0 + 3 139 1 0.52526 700.0 + 3 141 1 0.63909 700.0 + 5 28 1 0.65838 700.0 + 5 30 1 0.53473 700.0 + 5 32 1 0.39421 700.0 + 5 34 1 0.65255 700.0 + 5 36 1 0.72981 700.0 + 5 134 1 0.82177 700.0 + 5 136 1 0.71995 700.0 + 5 139 1 0.54535 700.0 + 5 141 1 0.51456 700.0 + 5 143 1 0.70606 700.0 + 5 145 1 0.79601 700.0 + 7 26 1 0.72851 700.0 + 7 28 1 0.51716 700.0 + 7 30 1 0.60935 700.0 + 7 32 1 0.639 700.0 + 7 139 1 0.64228 700.0 + 7 141 1 0.47894 700.0 + 7 143 1 0.46288 700.0 + 7 145 1 0.48298 700.0 + 7 147 1 0.79509 700.0 + 11 23 1 0.66279 700.0 + 11 26 1 0.50081 700.0 + 11 28 1 0.367 700.0 + 11 30 1 0.63828 700.0 + 11 32 1 0.79948 700.0 + 11 141 1 0.81808 700.0 + 11 143 1 0.65908 700.0 + 11 145 1 0.47919 700.0 + 11 147 1 0.64093 700.0 + 11 151 1 0.70852 700.0 + 13 20 1 0.80847 700.0 + 13 22 1 0.71803 700.0 + 13 23 1 0.55811 700.0 + 13 26 1 0.60187 700.0 + 13 28 1 0.64989 700.0 + 13 93 1 0.83621 700.0 + 13 143 1 0.73509 700.0 + 13 145 1 0.49084 700.0 + 13 147 1 0.48357 700.0 + 13 151 1 0.4828 700.0 + 13 153 1 0.82113 700.0 + 16 22 1 0.5072 700.0 + 16 23 1 0.43248 700.0 + 16 26 1 0.67013 700.0 + 16 28 1 0.83363 700.0 + 16 145 1 0.8099 700.0 + 16 147 1 0.69068 700.0 + 16 151 1 0.50947 700.0 + 16 153 1 0.76524 700.0 + 18 23 1 0.63997 700.0 + 18 151 1 0.68432 700.0 + 18 153 1 0.80808 700.0 + 18 155 1 0.89362 700.0 + 20 26 1 0.84876 700.0 + 23 151 1 0.89579 700.0 + 28 145 1 0.82961 700.0 + 32 61 1 0.86563 700.0 + 34 54 1 0.86666 700.0 + 34 61 1 0.8444 700.0 + 36 42 1 0.81992 700.0 + 36 44 1 0.77047 700.0 + 38 44 1 0.48671 700.0 + 38 46 1 0.75843 700.0 + 38 117 1 0.86118 700.0 + 38 119 1 0.71726 700.0 + 38 121 1 0.86818 700.0 + 38 132 1 0.86389 700.0 + 40 46 1 0.7332 700.0 + 40 117 1 0.62247 700.0 + 40 119 1 0.46895 700.0 + 40 121 1 0.54522 700.0 + 40 123 1 0.83125 700.0 + 40 130 1 0.86477 700.0 + 40 132 1 0.69301 700.0 + 40 134 1 0.85393 700.0 + 42 114 1 0.81266 700.0 + 42 117 1 0.60214 700.0 + 42 119 1 0.63007 700.0 + 42 121 1 0.70763 700.0 + 44 50 1 0.79126 700.0 + 44 52 1 0.6973 700.0 + 44 54 1 0.79849 700.0 + 44 113 1 0.84674 700.0 + 44 114 1 0.66404 700.0 + 44 117 1 0.50669 700.0 + 44 119 1 0.56936 700.0 + 44 121 1 0.7636 700.0 + 46 52 1 0.47856 700.0 + 46 54 1 0.61291 700.0 + 46 56 1 0.83363 700.0 + 46 109 1 0.79747 700.0 + 46 111 1 0.61498 700.0 + 46 113 1 0.63921 700.0 + 46 114 1 0.5188 700.0 + 46 117 1 0.52958 700.0 + 46 119 1 0.68981 700.0 + 48 54 1 0.4905 700.0 + 48 56 1 0.62009 700.0 + 48 59 1 0.82759 700.0 + 48 91 1 0.89644 700.0 + 48 107 1 0.74069 700.0 + 48 109 1 0.59121 700.0 + 48 111 1 0.43511 700.0 + 48 113 1 0.64112 700.0 + 48 114 1 0.56426 700.0 + 48 117 1 0.66665 700.0 + 48 119 1 0.81122 700.0 + 50 56 1 0.49446 700.0 + 50 59 1 0.62831 700.0 + 50 61 1 0.84443 700.0 + 50 80 1 0.81636 700.0 + 50 109 1 0.79028 700.0 + 50 111 1 0.52714 700.0 + 50 113 1 0.74668 700.0 + 50 114 1 0.77334 700.0 + 52 59 1 0.47927 700.0 + 52 61 1 0.62338 700.0 + 52 64 1 0.82307 700.0 + 52 111 1 0.80551 700.0 + 54 61 1 0.48743 700.0 + 54 64 1 0.62142 700.0 + 54 66 1 0.82288 700.0 + 54 111 1 0.89807 700.0 + 56 64 1 0.48405 700.0 + 56 66 1 0.61625 700.0 + 56 68 1 0.82142 700.0 + 56 76 1 0.73918 700.0 + 56 78 1 0.74012 700.0 + 56 80 1 0.60768 700.0 + 56 86 1 0.7852 700.0 + 59 66 1 0.48124 700.0 + 59 68 1 0.60416 700.0 + 59 70 1 0.82144 700.0 + 59 75 1 0.86909 700.0 + 59 76 1 0.7596 700.0 + 59 78 1 0.80881 700.0 + 59 80 1 0.75947 700.0 + 61 68 1 0.47968 700.0 + 61 70 1 0.60676 700.0 + 61 73 1 0.79275 700.0 + 61 75 1 0.85521 700.0 + 61 76 1 0.81241 700.0 + 64 70 1 0.48322 700.0 + 64 73 1 0.54297 700.0 + 64 75 1 0.61919 700.0 + 64 76 1 0.56063 700.0 + 64 78 1 0.7661 700.0 + 64 80 1 0.84434 700.0 + 66 73 1 0.47174 700.0 + 66 75 1 0.41238 700.0 + 66 76 1 0.4323 700.0 + 66 78 1 0.64907 700.0 + 66 80 1 0.80741 700.0 + 68 75 1 0.57819 700.0 + 68 76 1 0.71125 700.0 + 70 76 1 0.76145 700.0 + 73 78 1 0.84942 700.0 + 75 80 1 0.8858 700.0 + 76 82 1 0.79776 700.0 + 76 84 1 0.7149 700.0 + 76 86 1 0.80584 700.0 + 78 84 1 0.50753 700.0 + 78 86 1 0.64626 700.0 + 78 157 1 0.86034 700.0 + 80 86 1 0.47678 700.0 + 80 88 1 0.81941 700.0 + 80 157 1 0.85848 700.0 + 82 88 1 0.81685 700.0 + 82 155 1 0.85669 700.0 + 82 157 1 0.63824 700.0 + 82 160 1 0.80062 700.0 + 84 153 1 0.65633 700.0 + 84 155 1 0.53646 700.0 + 84 157 1 0.40121 700.0 + 84 160 1 0.64471 700.0 + 84 162 1 0.86851 700.0 + 86 107 1 0.88206 700.0 + 86 151 1 0.74807 700.0 + 86 153 1 0.54662 700.0 + 86 155 1 0.60798 700.0 + 86 157 1 0.60519 700.0 + 88 105 1 0.79393 700.0 + 88 107 1 0.71351 700.0 + 88 147 1 0.6237 700.0 + 88 151 1 0.51304 700.0 + 88 153 1 0.36389 700.0 + 88 155 1 0.60466 700.0 + 88 157 1 0.7518 700.0 + 91 101 1 0.88428 700.0 + 91 102 1 0.64908 700.0 + 91 105 1 0.5334 700.0 + 91 107 1 0.46342 700.0 + 91 109 1 0.77426 700.0 + 91 145 1 0.73855 700.0 + 91 147 1 0.51375 700.0 + 91 151 1 0.6283 700.0 + 91 153 1 0.64121 700.0 + 93 101 1 0.6494 700.0 + 93 102 1 0.51391 700.0 + 93 105 1 0.61096 700.0 + 93 107 1 0.67582 700.0 + 93 143 1 0.72748 700.0 + 93 145 1 0.51773 700.0 + 93 147 1 0.36355 700.0 + 93 151 1 0.65966 700.0 + 93 153 1 0.80249 700.0 + 95 102 1 0.37224 700.0 + 95 105 1 0.61558 700.0 + 95 107 1 0.75664 700.0 + 95 125 1 0.80789 700.0 + 95 143 1 0.7421 700.0 + 95 145 1 0.70028 700.0 + 95 147 1 0.69157 700.0 + 99 105 1 0.79249 700.0 + 99 125 1 0.87924 700.0 +102 147 1 0.86749 700.0 +107 113 1 0.87576 700.0 +107 114 1 0.78359 700.0 +107 117 1 0.8932 700.0 +109 114 1 0.49623 700.0 +109 117 1 0.71568 700.0 +111 117 1 0.73711 700.0 +114 121 1 0.8033 700.0 +114 123 1 0.73146 700.0 +117 123 1 0.50145 700.0 +117 125 1 0.67295 700.0 +117 130 1 0.85649 700.0 +117 132 1 0.84859 700.0 +119 125 1 0.49737 700.0 +119 130 1 0.5836 700.0 +119 132 1 0.51844 700.0 +119 134 1 0.81893 700.0 +121 130 1 0.49006 700.0 +121 132 1 0.54903 700.0 +121 134 1 0.86097 700.0 +123 132 1 0.72776 700.0 +125 134 1 0.85403 700.0 +132 139 1 0.83683 700.0 +132 141 1 0.7407 700.0 +132 143 1 0.89133 700.0 +134 141 1 0.54544 700.0 +134 143 1 0.81551 700.0 +136 143 1 0.86914 700.0 +157 165 1 0.82967 700.0 +160 166 1 0.81131 700.0 + +; Short elastic bonds for extended regions + 3 7 1 0.640 2500 + 5 11 1 0.640 2500 + 7 13 1 0.640 2500 + 11 16 1 0.640 2500 + 26 30 1 0.640 2500 + 28 32 1 0.640 2500 + 30 34 1 0.640 2500 + 86 91 1 0.640 2500 + 88 93 1 0.640 2500 + 91 95 1 0.640 2500 +143 147 1 0.640 2500 +145 151 1 0.640 2500 +147 153 1 0.640 2500 +151 155 1 0.640 2500 + +; Side chain bonds + 1 2 1 0.40 2500 + 3 4 1 0.400 5000 + 7 8 1 0.325 7500 + 13 14 1 0.330 5000 + 14 15 1 0.360 5000 + 18 19 1 0.363 7500 + 23 24 1 0.330 5000 + 24 25 1 0.360 5000 + 32 33 1 0.363 7500 + 34 35 1 0.400 5000 + 38 39 1 0.400 5000 + 40 41 1 0.330 7500 + 42 43 1 0.287 7500 + 44 45 1 0.352 7500 + 50 51 1 0.400 5000 + 52 53 1 0.352 5000 + 56 57 1 0.330 5000 + 57 58 1 0.360 5000 + 61 62 1 0.330 5000 + 62 63 1 0.360 5000 + 66 67 1 0.400 5000 + 68 69 1 0.352 7500 + 70 71 1 0.330 5000 + 71 72 1 0.360 5000 + 73 74 1 0.400 5000 + 78 79 1 0.330 7500 + 80 81 1 0.330 7500 + 82 83 1 0.352 7500 + 84 85 1 0.400 5000 + 86 87 1 0.400 5000 + 88 89 1 0.330 5000 + 89 90 1 0.380 5000 + 91 92 1 0.363 7500 + 95 96 1 0.325 7500 +102 103 1 0.330 5000 +103 104 1 0.360 5000 +105 106 1 0.400 5000 +107 108 1 0.363 7500 +109 110 1 0.400 5000 +111 112 1 0.352 7500 +114 115 1 0.330 5000 +115 116 1 0.380 5000 +119 120 1 0.363 7500 +121 122 1 0.287 7500 +123 124 1 0.352 7500 +125 126 1 0.325 5000 +130 131 1 0.352 5000 +134 135 1 0.400 5000 +136 137 1 0.330 5000 +137 138 1 0.360 5000 +139 140 1 0.400 5000 +141 142 1 0.287 7500 +145 146 1 0.363 7500 +147 148 1 0.336 7500 +151 152 1 0.363 7500 +155 156 1 0.363 7500 +157 158 1 0.330 5000 +158 159 1 0.380 5000 +160 161 1 0.363 7500 +162 163 1 0.330 5000 +163 164 1 0.380 5000 + +#ifdef FLEXIBLE +; Side chain bonds + 5 6 1 0.341 1000000 + 8 9 1 0.340 1000000 + 8 10 1 0.340 1000000 + 9 10 1 0.290 1000000 + 11 12 1 0.292 1000000 + 16 17 1 0.305 1000000 + 20 21 1 0.305 1000000 + 26 27 1 0.305 1000000 + 28 29 1 0.341 1000000 + 30 31 1 0.305 1000000 + 36 37 1 0.292 1000000 + 46 47 1 0.305 1000000 + 48 49 1 0.341 1000000 + 54 55 1 0.292 1000000 + 59 60 1 0.270 1000000 + 64 65 1 0.341 1000000 + 76 77 1 0.341 1000000 + 93 94 1 0.341 1000000 + 96 97 1 0.340 1000000 + 96 98 1 0.340 1000000 + 97 98 1 0.290 1000000 + 99 100 1 0.270 1000000 +117 118 1 0.305 1000000 +126 127 1 0.300 1000000 +126 128 1 0.300 1000000 +127 129 1 0.285 1000000 +128 129 1 0.285 1000000 +127 128 1 0.300 1000000 +132 133 1 0.341 1000000 +143 144 1 0.305 1000000 +148 149 1 0.320 1000000 +148 150 1 0.300 1000000 +149 150 1 0.270 1000000 +153 154 1 0.292 1000000 +#endif + +[ constraints ] +; Backbone bonds + 46 48 1 0.33 + 48 50 1 0.310 + 50 52 1 0.310 + 52 54 1 0.310 + 54 56 1 0.310 + 56 59 1 0.310 + 59 61 1 0.310 + 61 64 1 0.310 + 64 66 1 0.310 + 66 68 1 0.310 + 68 70 1 0.310 + 70 73 1 0.310 + 73 75 1 0.33 + 78 80 1 0.33 + 80 82 1 0.310 + 82 84 1 0.310 + 84 86 1 0.33 +119 121 1 0.33 +121 123 1 0.310 +123 125 1 0.310 +125 130 1 0.33 + +#ifndef FLEXIBLE +; Side chain bonds + 5 6 1 0.341 + 8 9 1 0.340 + 8 10 1 0.340 + 9 10 1 0.290 + 11 12 1 0.292 + 16 17 1 0.305 + 20 21 1 0.305 + 26 27 1 0.305 + 28 29 1 0.341 + 30 31 1 0.305 + 36 37 1 0.292 + 46 47 1 0.305 + 48 49 1 0.341 + 54 55 1 0.292 + 59 60 1 0.270 + 64 65 1 0.341 + 76 77 1 0.341 + 93 94 1 0.341 + 96 97 1 0.340 + 96 98 1 0.340 + 97 98 1 0.290 + 99 100 1 0.270 +117 118 1 0.305 +126 127 1 0.300 +126 128 1 0.300 +127 129 1 0.285 +128 129 1 0.285 +127 128 1 0.300 +132 133 1 0.341 +143 144 1 0.305 +148 149 1 0.320 +148 150 1 0.300 +149 150 1 0.270 +153 154 1 0.292 +#endif + +[ angles ] +; BBB angles + 44 46 48 10 130 20 + 46 48 50 10 134 25 + 48 50 52 2 96 700 + 50 52 54 2 96 700 + 52 54 56 2 96 700 + 54 56 59 2 96 700 + 56 59 61 2 96 700 + 59 61 64 2 96 700 + 61 64 66 2 96 700 + 64 66 68 2 96 700 + 66 68 70 2 96 700 + 68 70 73 2 96 700 + 70 73 75 10 127 20 + 73 75 76 10 127 20 + 76 78 80 10 127 20 + 78 80 82 10 98 100 + 80 82 84 2 98 100 + 82 84 86 10 134 25 + 84 86 88 10 134 25 +117 119 121 10 100 20 +119 121 123 10 100 20 +121 123 125 2 96 700 +123 125 130 10 100 20 +125 130 132 10 100 20 + 1 3 5 10 127 20 + 3 5 7 10 134 25 + 5 7 11 10 134 25 + 7 11 13 10 134 25 + 11 13 16 10 134 25 + 13 16 18 10 100 20 + 16 18 20 10 100 20 + 22 23 26 10 127 20 + 23 26 28 10 127 20 + 26 28 30 10 134 25 + 28 30 32 10 134 25 + 30 32 34 10 134 25 + 32 34 36 10 127 20 + 34 36 38 10 127 20 + 42 44 46 10 100 20 + 86 88 91 10 134 25 + 88 91 93 10 134 25 + 91 93 95 10 134 25 + 93 95 99 10 100 20 + 95 99 101 10 100 20 + 99 101 102 10 100 20 +101 102 105 10 100 20 +102 105 107 10 127 20 +105 107 109 10 127 20 +113 114 117 10 100 20 +114 117 119 10 100 20 +139 141 143 10 100 20 +141 143 145 10 127 20 +143 145 147 10 134 25 +145 147 151 10 134 25 +147 151 153 10 134 25 +151 153 155 10 134 25 +153 155 157 10 127 20 +155 157 160 10 127 20 + 75 76 78 10 127 20 + 36 38 40 10 127 20 + 38 40 42 10 100 20 + 40 42 44 10 100 20 + 18 20 22 10 100 20 + 20 22 23 10 100 20 +111 113 114 10 100 20 +157 160 162 10 127 20 +160 162 165 10 127 20 +162 165 166 10 127 20 +107 109 111 10 100 20 +109 111 113 10 100 20 +130 132 134 10 100 20 +132 134 136 10 100 20 +134 136 139 10 100 20 +136 139 141 10 100 20 + +; BBS angles regular martini + 1 3 4 2 100 25 + 3 5 6 2 100 25 + 5 7 8 2 100 25 + 7 11 12 2 100 25 + 11 13 14 2 100 25 + 13 16 17 2 100 25 + 16 18 19 2 100 25 + 18 20 21 2 100 25 + 22 23 24 2 100 25 + 23 26 27 2 100 25 + 26 28 29 2 100 25 + 28 30 31 2 100 25 + 30 32 33 2 100 25 + 32 34 35 2 100 25 + 34 36 37 2 100 25 + 36 38 39 2 100 25 + 38 40 41 2 100 25 + 40 42 43 2 100 25 + 42 44 45 2 100 25 + 44 46 47 2 100 25 + 46 48 49 2 100 25 + 48 50 51 2 100 25 + 50 52 53 2 100 25 + 52 54 55 2 100 25 + 54 56 57 2 100 25 + 56 59 60 2 100 25 + 59 61 62 2 100 25 + 61 64 65 2 100 25 + 64 66 67 2 100 25 + 66 68 69 2 100 25 + 68 70 71 2 100 25 + 70 73 74 2 100 25 + 75 76 77 2 100 25 + 76 78 79 2 100 25 + 78 80 81 2 100 25 + 80 82 83 2 100 25 + 82 84 85 2 100 25 + 84 86 87 2 100 25 + 86 88 89 2 100 25 + 88 91 92 2 100 25 + 91 93 94 2 100 25 + 93 95 96 2 100 25 + 95 99 100 2 100 25 +101 102 103 2 100 25 +102 105 106 2 100 25 +105 107 108 2 100 25 +107 109 110 2 100 25 +109 111 112 2 100 25 +113 114 115 2 100 25 +114 117 118 2 100 25 +117 119 120 2 100 25 +119 121 122 2 100 25 +121 123 124 2 100 25 +123 125 126 2 100 25 +125 130 131 2 100 25 +130 132 133 2 100 25 +132 134 135 2 100 25 +134 136 137 2 100 25 +136 139 140 2 100 25 +139 141 142 2 100 25 +141 143 144 2 100 25 +143 145 146 2 100 25 +145 147 148 2 100 25 +147 151 152 2 100 25 +151 153 154 2 100 25 +153 155 156 2 100 25 +155 157 158 2 100 25 +157 160 161 2 100 25 +160 162 163 2 100 25 + +; First SBB regular martini + 2 1 3 2 100 25 + +; SC-BB-BB and BB-BB-SC scFix + 2 1 3 10 100 15 ; SC-BB-BB + 4 3 5 10 100 15 ; SC-BB-BB + 6 5 7 10 100 15 ; SC-BB-BB + 8 7 11 10 100 15 ; SC-BB-BB + 12 11 13 10 100 15 ; SC-BB-BB + 14 13 16 10 100 15 ; SC-BB-BB + 17 16 18 10 100 15 ; SC-BB-BB + 19 18 20 10 100 15 ; SC-BB-BB + 21 20 22 10 100 15 ; SC-BB-BB + 24 23 26 10 100 15 ; SC-BB-BB + 27 26 28 10 100 15 ; SC-BB-BB + 29 28 30 10 100 15 ; SC-BB-BB + 31 30 32 10 100 15 ; SC-BB-BB + 33 32 34 10 100 15 ; SC-BB-BB + 35 34 36 10 100 15 ; SC-BB-BB + 37 36 38 10 100 15 ; SC-BB-BB + 39 38 40 10 100 15 ; SC-BB-BB + 41 40 42 10 100 15 ; SC-BB-BB + 43 42 44 10 100 15 ; SC-BB-BB + 45 44 46 10 100 15 ; SC-BB-BB + 47 46 48 10 100 15 ; SC-BB-BB + 49 48 50 10 100 15 ; SC-BB-BB + 51 50 52 10 100 15 ; SC-BB-BB + 53 52 54 10 100 15 ; SC-BB-BB + 55 54 56 10 100 15 ; SC-BB-BB + 57 56 59 10 100 15 ; SC-BB-BB + 60 59 61 10 100 15 ; SC-BB-BB + 62 61 64 10 100 15 ; SC-BB-BB + 65 64 66 10 100 15 ; SC-BB-BB + 67 66 68 10 100 15 ; SC-BB-BB + 69 68 70 10 100 15 ; SC-BB-BB + 71 70 73 10 100 15 ; SC-BB-BB + 74 73 75 10 100 15 ; SC-BB-BB + 77 76 78 10 100 15 ; SC-BB-BB + 79 78 80 10 100 15 ; SC-BB-BB + 81 80 82 10 100 15 ; SC-BB-BB + 83 82 84 10 100 15 ; SC-BB-BB + 85 84 86 10 100 15 ; SC-BB-BB + 87 86 88 10 100 15 ; SC-BB-BB + 89 88 91 10 100 15 ; SC-BB-BB + 92 91 93 10 100 15 ; SC-BB-BB + 94 93 95 10 100 15 ; SC-BB-BB + 96 95 99 10 100 15 ; SC-BB-BB +100 99 101 10 100 15 ; SC-BB-BB +103 102 105 10 100 15 ; SC-BB-BB +106 105 107 10 100 15 ; SC-BB-BB +108 107 109 10 100 15 ; SC-BB-BB +110 109 111 10 100 15 ; SC-BB-BB +112 111 113 10 100 15 ; SC-BB-BB +115 114 117 10 100 15 ; SC-BB-BB +118 117 119 10 100 15 ; SC-BB-BB +120 119 121 10 100 15 ; SC-BB-BB +122 121 123 10 100 15 ; SC-BB-BB +124 123 125 10 100 15 ; SC-BB-BB +126 125 130 10 100 15 ; SC-BB-BB +131 130 132 10 100 15 ; SC-BB-BB +133 132 134 10 100 15 ; SC-BB-BB +135 134 136 10 100 15 ; SC-BB-BB +137 136 139 10 100 15 ; SC-BB-BB +140 139 141 10 100 15 ; SC-BB-BB +142 141 143 10 100 15 ; SC-BB-BB +144 143 145 10 100 15 ; SC-BB-BB +146 145 147 10 100 15 ; SC-BB-BB +148 147 151 10 100 15 ; SC-BB-BB +152 151 153 10 100 15 ; SC-BB-BB +154 153 155 10 100 15 ; SC-BB-BB +156 155 157 10 100 15 ; SC-BB-BB +158 157 160 10 100 15 ; SC-BB-BB +161 160 162 10 100 15 ; SC-BB-BB +163 162 165 10 100 15 ; SC-BB-BB + 1 3 4 10 100 15 ; BB-BB-SC + 3 5 6 10 100 15 ; BB-BB-SC + 5 7 8 10 100 15 ; BB-BB-SC + 7 11 12 10 100 15 ; BB-BB-SC + 11 13 14 10 100 15 ; BB-BB-SC + 13 16 17 10 100 15 ; BB-BB-SC + 16 18 19 10 100 15 ; BB-BB-SC + 18 20 21 10 100 15 ; BB-BB-SC + 22 23 24 10 100 15 ; BB-BB-SC + 23 26 27 10 100 15 ; BB-BB-SC + 26 28 29 10 100 15 ; BB-BB-SC + 28 30 31 10 100 15 ; BB-BB-SC + 30 32 33 10 100 15 ; BB-BB-SC + 32 34 35 10 100 15 ; BB-BB-SC + 34 36 37 10 100 15 ; BB-BB-SC + 36 38 39 10 100 15 ; BB-BB-SC + 38 40 41 10 100 15 ; BB-BB-SC + 40 42 43 10 100 15 ; BB-BB-SC + 42 44 45 10 100 15 ; BB-BB-SC + 44 46 47 10 100 15 ; BB-BB-SC + 46 48 49 10 100 15 ; BB-BB-SC + 48 50 51 10 100 15 ; BB-BB-SC + 50 52 53 10 100 15 ; BB-BB-SC + 52 54 55 10 100 15 ; BB-BB-SC + 54 56 57 10 100 15 ; BB-BB-SC + 56 59 60 10 100 15 ; BB-BB-SC + 59 61 62 10 100 15 ; BB-BB-SC + 61 64 65 10 100 15 ; BB-BB-SC + 64 66 67 10 100 15 ; BB-BB-SC + 66 68 69 10 100 15 ; BB-BB-SC + 68 70 71 10 100 15 ; BB-BB-SC + 70 73 74 10 100 15 ; BB-BB-SC + 75 76 77 10 100 15 ; BB-BB-SC + 76 78 79 10 100 15 ; BB-BB-SC + 78 80 81 10 100 15 ; BB-BB-SC + 80 82 83 10 100 15 ; BB-BB-SC + 82 84 85 10 100 15 ; BB-BB-SC + 84 86 87 10 100 15 ; BB-BB-SC + 86 88 89 10 100 15 ; BB-BB-SC + 88 91 92 10 100 15 ; BB-BB-SC + 91 93 94 10 100 15 ; BB-BB-SC + 93 95 96 10 100 15 ; BB-BB-SC + 95 99 100 10 100 15 ; BB-BB-SC +101 102 103 10 100 15 ; BB-BB-SC +102 105 106 10 100 15 ; BB-BB-SC +105 107 108 10 100 15 ; BB-BB-SC +107 109 110 10 100 15 ; BB-BB-SC +109 111 112 10 100 15 ; BB-BB-SC +113 114 115 10 100 15 ; BB-BB-SC +114 117 118 10 100 15 ; BB-BB-SC +117 119 120 10 100 15 ; BB-BB-SC +119 121 122 10 100 15 ; BB-BB-SC +121 123 124 10 100 15 ; BB-BB-SC +123 125 126 10 100 15 ; BB-BB-SC +125 130 131 10 100 15 ; BB-BB-SC +130 132 133 10 100 15 ; BB-BB-SC +132 134 135 10 100 15 ; BB-BB-SC +134 136 137 10 100 15 ; BB-BB-SC +136 139 140 10 100 15 ; BB-BB-SC +139 141 142 10 100 15 ; BB-BB-SC +141 143 144 10 100 15 ; BB-BB-SC +143 145 146 10 100 15 ; BB-BB-SC +145 147 148 10 100 15 ; BB-BB-SC +147 151 152 10 100 15 ; BB-BB-SC +151 153 154 10 100 15 ; BB-BB-SC +153 155 156 10 100 15 ; BB-BB-SC +155 157 158 10 100 15 ; BB-BB-SC +157 160 161 10 100 15 ; BB-BB-SC +160 162 163 10 100 15 ; BB-BB-SC + +; Side chain angles + 7 8 9 2 120.000 50.0 + 7 8 10 2 120.000 50.0 + 13 14 15 2 180.000 25.0 + 23 24 25 2 180.000 25.0 + 56 57 58 2 180.000 25.0 + 61 62 63 2 180.000 25.0 + 70 71 72 2 180.000 25.0 + 88 89 90 2 180.000 25.0 + 95 96 97 2 120.000 50.0 + 95 96 98 2 120.000 50.0 +102 103 104 2 180.000 25.0 +114 115 116 2 180.000 25.0 +125 126 127 2 120.000 60.0 +125 126 128 2 120.000 60.0 +136 137 138 2 180.000 25.0 +147 148 149 2 120.000 50.0 +147 148 150 2 120.000 50.0 +157 158 159 2 180.000 25.0 +162 163 164 2 180.000 25.0 + +[ dihedrals ] + 48 50 52 54 1 -120 400 1 + 50 52 54 56 1 -120 400 1 + 52 54 56 59 1 -120 400 1 + 54 56 59 61 1 -120 400 1 + 56 59 61 64 1 -120 400 1 + 59 61 64 66 1 -120 400 1 + 61 64 66 68 1 -120 400 1 + 64 66 68 70 1 -120 400 1 + 66 68 70 73 1 -120 400 1 + +; SC-BB-BB-SC scFix + 2 1 3 4 1 17.5 75 1 ; SC-BB-BB-SC + 4 3 5 6 1 6.4 75 1 ; SC-BB-BB-SC + 6 5 7 8 1 27.5 75 1 ; SC-BB-BB-SC + 8 7 11 12 1 18.9 75 1 ; SC-BB-BB-SC + 12 11 13 14 1 25.1 75 1 ; SC-BB-BB-SC + 14 13 16 17 1 38.3 75 1 ; SC-BB-BB-SC + 17 16 18 19 1 66.1 75 1 ; SC-BB-BB-SC + 19 18 20 21 1 -135.5 75 1 ; SC-BB-BB-SC + 24 23 26 27 1 1.9 75 1 ; SC-BB-BB-SC + 27 26 28 29 1 36.6 75 1 ; SC-BB-BB-SC + 29 28 30 31 1 35.8 75 1 ; SC-BB-BB-SC + 31 30 32 33 1 6.1 75 1 ; SC-BB-BB-SC + 33 32 34 35 1 29.4 75 1 ; SC-BB-BB-SC + 35 34 36 37 1 22.0 75 1 ; SC-BB-BB-SC + 37 36 38 39 1 7.5 75 1 ; SC-BB-BB-SC + 39 38 40 41 1 130.2 75 1 ; SC-BB-BB-SC + 41 40 42 43 1 -176.4 75 1 ; SC-BB-BB-SC + 43 42 44 45 1 -171.2 75 1 ; SC-BB-BB-SC + 45 44 46 47 1 76.6 75 1 ; SC-BB-BB-SC + 47 46 48 49 1 68.1 75 1 ; SC-BB-BB-SC + 49 48 50 51 1 -108.2 75 1 ; SC-BB-BB-SC + 51 50 52 53 1 -134.5 75 1 ; SC-BB-BB-SC + 53 52 54 55 1 -107.0 75 1 ; SC-BB-BB-SC + 55 54 56 57 1 -137.9 75 1 ; SC-BB-BB-SC + 57 56 59 60 1 -141.7 75 1 ; SC-BB-BB-SC + 60 59 61 62 1 -143.5 75 1 ; SC-BB-BB-SC + 62 61 64 65 1 -158.3 75 1 ; SC-BB-BB-SC + 65 64 66 67 1 -126.3 75 1 ; SC-BB-BB-SC + 67 66 68 69 1 -133.4 75 1 ; SC-BB-BB-SC + 69 68 70 71 1 -121.0 75 1 ; SC-BB-BB-SC + 71 70 73 74 1 148.8 75 1 ; SC-BB-BB-SC + 77 76 78 79 1 79.6 75 1 ; SC-BB-BB-SC + 79 78 80 81 1 78.1 75 1 ; SC-BB-BB-SC + 81 80 82 83 1 -165.6 75 1 ; SC-BB-BB-SC + 83 82 84 85 1 -134.9 75 1 ; SC-BB-BB-SC + 85 84 86 87 1 -164.8 75 1 ; SC-BB-BB-SC + 87 86 88 89 1 1.6 75 1 ; SC-BB-BB-SC + 89 88 91 92 1 9.2 75 1 ; SC-BB-BB-SC + 92 91 93 94 1 21.9 75 1 ; SC-BB-BB-SC + 94 93 95 96 1 -2.8 75 1 ; SC-BB-BB-SC + 96 95 99 100 1 -166.4 75 1 ; SC-BB-BB-SC +103 102 105 106 1 28.2 75 1 ; SC-BB-BB-SC +106 105 107 108 1 43.4 75 1 ; SC-BB-BB-SC +108 107 109 110 1 40.0 75 1 ; SC-BB-BB-SC +110 109 111 112 1 89.1 75 1 ; SC-BB-BB-SC +115 114 117 118 1 72.7 75 1 ; SC-BB-BB-SC +118 117 119 120 1 78.6 75 1 ; SC-BB-BB-SC +120 119 121 122 1 -115.8 75 1 ; SC-BB-BB-SC +122 121 123 124 1 -150.5 75 1 ; SC-BB-BB-SC +124 123 125 126 1 167.2 75 1 ; SC-BB-BB-SC +126 125 130 131 1 18.4 75 1 ; SC-BB-BB-SC +131 130 132 133 1 -18.9 75 1 ; SC-BB-BB-SC +133 132 134 135 1 22.5 75 1 ; SC-BB-BB-SC +135 134 136 137 1 126.1 75 1 ; SC-BB-BB-SC +137 136 139 140 1 -172.1 75 1 ; SC-BB-BB-SC +140 139 141 142 1 53.0 75 1 ; SC-BB-BB-SC +142 141 143 144 1 26.5 75 1 ; SC-BB-BB-SC +144 143 145 146 1 32.8 75 1 ; SC-BB-BB-SC +146 145 147 148 1 37.6 75 1 ; SC-BB-BB-SC +148 147 151 152 1 18.0 75 1 ; SC-BB-BB-SC +152 151 153 154 1 -1.3 75 1 ; SC-BB-BB-SC +154 153 155 156 1 32.1 75 1 ; SC-BB-BB-SC +156 155 157 158 1 47.3 75 1 ; SC-BB-BB-SC +158 157 160 161 1 -11.0 75 1 ; SC-BB-BB-SC +161 160 162 163 1 48.3 75 1 ; SC-BB-BB-SC + 20 22 23 24 1 110.9 75 1 ; BB-BB-BB-SC + 21 20 22 23 1 -150.9 75 1 ; SC-BB-BB-BB + 73 75 76 77 1 133.7 75 1 ; BB-BB-BB-SC + 74 73 75 76 1 -144.5 75 1 ; SC-BB-BB-BB + 99 101 102 103 1 114.4 75 1 ; BB-BB-BB-SC +100 99 101 102 1 -105.5 75 1 ; SC-BB-BB-BB +111 113 114 115 1 74.0 75 1 ; BB-BB-BB-SC +112 111 113 114 1 3.8 75 1 ; SC-BB-BB-BB +163 162 165 166 1 137.2 75 1 ; SC-BB-BB-BB + +[ exclusions ] + 7 8 9 10 + 8 9 10 + 9 10 + 95 96 97 98 + 96 97 98 + 97 98 +125 126 127 128 129 +126 127 128 129 +127 128 129 +128 129 +147 148 149 150 +148 149 150 +149 150 + +[ dihedrals ] +129 127 128 126 2 180.0 50.0 + diff --git a/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/topol.top b/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/topol.top new file mode 100644 index 000000000..a45ed27af --- /dev/null +++ b/vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/topol.top @@ -0,0 +1,9 @@ + +#include "martini.itp" +#include "molecule_0.itp" + +[ system ] +Title of the system + +[ molecules ] +molecule_0 1 diff --git a/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/command index ef8631332..fb4201f8a 100644 --- a/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/command @@ -7,4 +7,4 @@ martinize2 -dssp -elastic -cys auto --scfix +-ef 500 diff --git a/vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/command index d217a1321..18cd9d249 100644 --- a/vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/command @@ -4,8 +4,8 @@ martinize2 -o cg.top -ff martini3001 -elastic --scfix -cys auto -dssp -from amber -resid input +-ef 500 diff --git a/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/command index 3a3f3e25d..ae9511f29 100644 --- a/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/command @@ -1 +1,9 @@ -martinize2 -f ../3i40.pdb -o cg.top -x cg.pdb -dssp -p backbone -ff martini3001 -scfix -cys auto -ignore HOH +martinize2 +-f ../3i40.pdb +-o cg.top +-x cg.pdb +-dssp +-p backbone +-ff martini3001 +-cys auto +-ignore HOH diff --git a/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/command index a4b4c5c7c..f79caf222 100644 --- a/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/command @@ -1 +1,13 @@ -martinize2 -f ../6LFO_gap.pdb -o cg.top -x cg.pdb -dssp -p backbone -ff martini3001 -scfix -cys auto -ignore HOH -elastic -eunit all -resid input +martinize2 +-f ../6LFO_gap.pdb +-o cg.top +-x cg.pdb +-dssp +-p backbone +-ff martini3001 +-cys auto +-ignore HOH +-elastic +-eunit all +-resid input +-ef 500 diff --git a/vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/command index 58b93113a..d3143449c 100644 --- a/vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/command @@ -1 +1,12 @@ -martinize2 -f ../aa.pdb -o cg.top -x cg.pdb -dssp -p backbone -ff martini3001 -scfix -cys auto -ignore HOH -elastic -eunit chain +martinize2 +-f ../aa.pdb +-o cg.top +-x cg.pdb +-dssp +-p backbone +-ff martini3001 +-cys auto +-ignore HOH +-elastic +-eunit chain +-ef 500 diff --git a/vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/command index 437d789de..6e2391252 100644 --- a/vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/command @@ -1 +1,12 @@ -martinize2 -f ../aa.pdb -o cg.top -x cg.pdb -dssp -p backbone -ff martini3001 -scfix -cys auto -ignore HOH -elastic -eunit 8:18 +martinize2 +-f ../aa.pdb +-o cg.top +-x cg.pdb +-dssp +-p backbone +-ff martini3001 +-cys auto +-ignore HOH +-elastic +-eunit 8:18 +-ef 500 diff --git a/vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/command index 7030c6c06..9b2d22276 100644 --- a/vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/command @@ -9,3 +9,5 @@ martinize2 -ep 2 -modify A-ASP50:ASP-HD2 -ignore HOH +-noscfix +-ef 500 diff --git a/vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/command index 3425fb3de..2f04be6aa 100644 --- a/vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/command @@ -8,3 +8,4 @@ martinize2 -water-bias-eps idr:0.5 -id-regions 1:24 -idr-tune +-noscfix diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/command index 489d88687..dadcf6ffd 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/command @@ -4,7 +4,7 @@ martinize2 -o topol.top -ff martini30b32 -elastic --scfix -cys auto -dssp -ignore HOH +-ef 500 \ No newline at end of file diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/command index 40e34be2e..694db48ec 100755 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/command @@ -9,4 +9,6 @@ martinize2 -ef 700 -eu 0.85 -water-bias --water-bias-eps E:-.5 C:1.0 H:-1.0 \ No newline at end of file +-water-bias-eps E:-.5 C:1.0 H:-1.0 +-noscfix +-cys none diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command index 31dd6a437..cdf208511 100755 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command @@ -6,3 +6,5 @@ martinize2 -ignore HOH -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC -go ../map.map +-noscfix +-cys none diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command index 17b5b458d..f0de2bf47 100755 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command @@ -8,3 +8,5 @@ martinize2 -go ../map.map -water-bias -water-bias-eps E:-.5 C:1.0 H:-1.0 +-noscfix +-cys none diff --git a/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/command index ce8dc5d13..143fdda0e 100644 --- a/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/command @@ -4,7 +4,7 @@ martinize2 -o topol.top -ff martini3001 -elastic --scfix -cys auto -dssp -ignore HOH +-ef 500 diff --git a/vermouth/tests/data/integration_tests/tier-1/villin/martinize2/command b/vermouth/tests/data/integration_tests/tier-1/villin/martinize2/command index 7d4b4d0b9..9a1dd2e9a 100644 --- a/vermouth/tests/data/integration_tests/tier-1/villin/martinize2/command +++ b/vermouth/tests/data/integration_tests/tier-1/villin/martinize2/command @@ -5,3 +5,4 @@ martinize2 -ff martini22p -mutate A-MET53:VAL -resid input +-noscfix diff --git a/vermouth/tests/integration_tests/test_integration.py b/vermouth/tests/integration_tests/test_integration.py index 63daf9f2f..6d06a1e7a 100644 --- a/vermouth/tests/integration_tests/test_integration.py +++ b/vermouth/tests/integration_tests/test_integration.py @@ -172,6 +172,7 @@ def _interaction_equal(interaction1, interaction2): ['tier-1', 'EN_chain'], ['tier-1', 'EN_region'], ['tier-1', 'hst5'], + ['tier-1', '1UBQ'] # ['tier-2', 'barnase_barstar'], # ['tier-2', 'dna'], # ['tier-2', 'gpa_dimer'], diff --git a/vermouth/tests/test_name_moltype.py b/vermouth/tests/test_name_moltype.py index 7f93670ce..6a18f834b 100644 --- a/vermouth/tests/test_name_moltype.py +++ b/vermouth/tests/test_name_moltype.py @@ -150,7 +150,7 @@ def test_martinize2_moltypes(tmp_path, deduplicate): '-f', str(PDB_HB), '-o', 'topol.top', '-x', 'out.pdb', - '-ignore', 'HOH', '-ignore', 'HEME', + '-ignore', 'HOH', '-ignore', 'HEME', '-noscfix', ] if deduplicate: expected = ['molecule_{}.itp'.format(i) for i in range(2)]