search

openforcefield / amber-ff-porting

Scratch space for porting amber FFs into SMIRNOFF format
1 stars 3 forks source link

Include CYM parameters in ff14sb port #42

Closed pbuslaev closed 9 months ago

pbuslaev commented 10 months ago

Those changes should solve #41

j-wags commented 10 months ago

Thanks for opening this. Unfortunately we don't have fancy automation on this repo to run everything in CI, so we'll need someone to reproduce the environment for this work and run it with the changes. We'll also need to extend the tests to validate the new parameters. I've put out a call for volunteers in our internal slack channel. Basically this will require 1) making an env suitable to run the porting code, 2) updating the porting code to handle CYM (may be done, or more may be required), and 3) validating the new parameters by extending the existing tests. I’m happy to advise on these steps and do the GitHub+conda stuff to push a new release once it’s done.

mikemhenry commented 9 months ago

I am working to make sure I have a pipeline that works locally, then I can test this PR.

mikemhenry commented 9 months ago

Also I think we will want to update the parameter_deduplication.ipynb notebook as well. I am not sure if we need CYM in the MainChain resnames or if it should be in the else: block, or even both.

for folder in ['MainChain', 'CTerminal', 'NTerminal']:
    if (folder == 'MainChain'):
      resnames = [ 'ALA', 'ARG', 'ASH', 'ASN', 'ASP', 'GLH', 'GLN', 'GLU', 'GLY',  'HID',                      'HIE', 'HIP', 'ILE', 'LEU', 'LYN', 'LYS', 'MET', 'PHE', 'PRO', 'SER',                       'THR', 'TYR', 'VAL', 'TRP',]

    else:
      resnames = [ 'ALA', 'ARG', 'ASN', 'ASP', 'GLN', 'GLU', 'GLY', 'HID', 'HIE', 'HIP',
                   'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TYR', 'VAL',                       'TRP', 'CYX' ]
j-wags commented 9 months ago

So, a quick update: