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martimunicoy / peleffy

The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.

Home Page:https://martimunicoy.github.io/peleffy

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Workflow to automatically parameterize protein residues

martimunicoy opened this issue · comments

commented

Design a workflow to generate automatically the parameters of standard protein residues with Open Force Field toolkit.

commented

We're making some progress on that here, if you'd like to follow along.

We don't have an OFFXML file for Amber FF14SB available publicly yet, and it will probably be another month or two before it's released. We are still trying to correct some energy discrepancies. But if you contact me directly on Slack I can send you our working version :-)

commented

We are currently planning to test the performance of openff-1.2.0.offxml for small molecules along with the OPLS2005 protein force field implemented in PELE. After that, the next step would be to use Amber (I have seen some examples of combining SMIRNOFF with Amber in your repository) or maybe use something like the approach you mentioned. I will contact you on Slack regarding this (an other stuff related with the GBSA parameters). Thank you :)