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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
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implement small molecule DB #456

Closed fgrunewald closed 2 years ago

fgrunewald commented 2 years ago

43 small molecules from Riccardo's small molecule DB together with their charmm files. This one depends on the EN fix

pckroon commented 2 years ago

Is there anything specific you need me to take a look at? 100k+ lines is a bit much to go through ;) Maybe add the appropriate citation?

fgrunewald commented 2 years ago

@pckroon I don't think so. It's just a bunch of parameters for the database

fgrunewald commented 2 years ago

Just to make sure, there doesn't need to be citation for these?

I meant you don't need to review; for sure I need to add the citations. But Siewert has a whishlist of data he wants to add. That goes all in here.

fgrunewald commented 2 years ago

Point of order on the phosphorylation. The additional bead is added at the end of the molecule not with the residue

pckroon commented 2 years ago

Is the HSD part of this PR? And the EN tests?

fgrunewald commented 2 years ago

Histidines, Phosphorylation, Cofactors, Small Molecule DB + one fix to the EN

pckroon commented 2 years ago

Point of order on the phosphorylation. The additional bead is added at the end of the molecule not with the residue

This happens because the new bead is assigned the next available atom ID, and at the end of martinize atoms are sorted by atom id. We could aggressively renumber atom ids, but is it an issue?

fgrunewald commented 2 years ago

Yeah this will be an issue for many people. It makes the files harder to read and also it messes with the residue completeness. Most analysis programs (falsely) assume atoms in one residue are consecutive. Perhaps it is even enforced by some file formats. But if it is not in the code now it is hard to add. I've been looking into it and this type of renumbering get's exteremly slow even for moderately large proteins. So I suggest since we don't have any modifications for the M3 FF yet, we just ignore this. But be prepared

pckroon commented 2 years ago

It may be an option to renumber only all the way at the end, when writing the pdb/itp. Shouldn't be /too/ hard. I'll pick that up for hacktoberfest

pckroon commented 2 years ago

I just noticed citations are still missing for these. Iff you can't get around to it today could you open an issue so we don't forget?