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GongCHEN-1995 / GB-FFs-Model

Graph-Based Force Fields Model to parameterize Force Fields by Graph Attention Networks
MIT License
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Adding ability to generate forcefield parameter file in other formats? #1

Open mchakra8 opened 1 month ago

mchakra8 commented 1 month ago

I read with great interest your recent publication (https://doi.org/10.1021/acs.jctc.3c01421), and followed the README information to create the necessary environment for running your codebase. However, I noticed that the only output format available in ParaFileGenerator.ipynb is *.prm, i.e., the parameter file format for Tinker. Given that the paper places focus on optimizing the General Amber Force Field (GAFF), is there any ongoing work or future plan to add the capability to output forcefield parameter files in Amber format (i.e., *.prep and *.frcmod)? Currently, the procedure for attempting this through the $AMBERHOME/bin/tinker_to_amber pipeline is not robust, requires that a prior installation of tinker be available to the user, and assumes that the user has already generated an *.analout file in tinker using analyze. ParmEd also does not seem to support this type of conversion.

GongCHEN-1995 commented 1 month ago

Since Tinker supports GAFF and our MD simulations are all performed on Tinker GPU, our code is designed to output only *.prm files.

I understand the convenience of having Amber-compatible output formats. However, at this stage, we recommend reaching out to the developers of Amber or Tinker to inquire about potential tools or updates that may facilitate the conversion of .prm files to .prep and *.frcmod formats for Amber.