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openmm / openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)
http://openmm.org
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Petition to support parameterization using `CGenFF` for small molecules #317

Open taoliu032 opened 7 months ago

taoliu032 commented 7 months ago

Hello,

First of all, thank you tremendously for developing the openmmforcefields tool, especially for allowing the on-the-fly parameterization using GAFF and others! It really saved a lot of pain of dealing with file format compatibility!

In terms of small molecule parameterization, besides the currently available options including GAFF, is there a plan to add support for CGenFF? With the current support for CHARMM force field, it would be really amazing to have CGenFF in the toolkit too :)

I saw a similar question in the FAQ section. I am not certain if there is a conda-installable tool for generating CGenFF parameters. Meanwhile, the CGenFF developers have built a tool and web server to streamline the parameterization process: https://docs.silcsbio.com/2023/cgenff/cgenff.html#usage and https://cgenff.silcsbio.com/. And it is also in CGenFF's developers' interest (and their future plan) to make their force field more widely used: https://cgenff.silcsbio.com/commonFiles/futureProspects.php

mattwthompson commented 7 months ago

Integrating CGenFF into this package would almost surely require a command-line tool or API that provides the result of force field parameterization. (Think along the lines of tleap and friends within AmberTools or the OpenFF Toolkit for SMIRNOFF force fields.) I haven't used CGenFF (or the CHARMM ecosystem) much does such a tool exist? Bonus points for a standalone tool not a part of a larger or monolithic software suite.

I haven't used a SilcsBio product myself - how is CGenFF licensed? Your second link is from 2018 and looks more like an academic website and less like the other pages with SilcsBio branding.