Open mchakra8 opened 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.
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 oftinker
be available to the user, and assumes that the user has already generated an*.analout
file intinker
usinganalyze
.ParmEd
also does not seem to support this type of conversion.