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corrected lines in go_models.rst for including go files in martini_v3…
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csbrasnett committed Oct 10, 2024
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4 changes: 2 additions & 2 deletions doc/source/tutorials/go_models.rst
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Expand Up @@ -73,9 +73,9 @@ depend on your protein)::
To activate your Go model, you can simply include these files in your master ``martini_v3.0.0.itp`` file with the
following commands::

sed -i "s/\[ nonbond_params \]/\#ifdef GO_VIRT\n\#include \"go_atomtype.itp\"\n\#endif\n\n\[ nonbond_params \]/" martini_v3.0.0.itp
sed -i "s/\[ nonbond_params \]/\#ifdef GO_VIRT\n\#include \"go_atomtypes.itp\"\n\#endif\n\n\[ nonbond_params \]/" martini_v3.0.0.itp

echo -e "\n#ifdef GO_VIRT \n#include \"go-table_VirtGoSites.itp\"\n#endif" >> martini_v3.0.0.itp
echo -e "\n#ifdef GO_VIRT \n#include \"go_nbparams.itp\"\n#endif" >> martini_v3.0.0.itp

The Go model should then be usable in your simulations following the `general protein tutorial <https://pubs.acs.org/doi/10.1021/acs.jctc.4c00677>`_.
But careful! While the Go model specifies nonbonded interactions, the interactions are only defined
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