Decorating proteins #363
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@cesar-lopez-bau you will probably not get around a little bit of scripting with python. The basic idea would be to create a .json file that describes your whole residue graph which is protein plus sugars. This graph needs to have each residue as a node and each node needs to have a Let me give you an example. For the sake of brevity let's generate a peptide with polyply. Note that Step 1 in your case is then replaced by martinize2. ===> Step 1
Now we generate a protein itp file using:
===> Step 2 Next we read in the fasta file and attache the PEG residues to the protein. The following code is an example on how to do this. Note that
==> Step 3: run the gen_params program
Please note that the PEO.martini3.ff is modified for the example at hand:
The coordinate generation works the same as in the PEGylated protein tutorial where you provide the coordinates of the CG protein to If you have all the links the only thing to do is to build a custom script like the one above that specifies where to attach them to the protein. We are working with Paulo on a graphical user interface to do this automatically but it will take a few month until it is released. Let me know what you think about it and if you have any more questions! Best, |
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Hi guys;
Is there a way to attached modifications into a martinize2 generated topology. Let's say I want to attach CG glycans for which I can add the parameters into the polyply library. Then I would think of indicating the attachment in the protein and outputting a new structure + glycosylation while adding the new parameters into the original itp. I tried following the PEGtylated protein tutorial but it is somehow inefficient if I want to add more than 1 decoration and for many proteins. Any help will be appreciated. Cesar
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