Is the PMX compatible with CHARM36 output I get from CGenFF server? The output folder contains mol2, err, and str. The other GROMACS output folder contains pdb, and top file along with ff related files. Am I suppose to put these files(which files or file type specifically?) into appropriate folder and run the fe.atom.mapping in Jupyter note? For AMBER, I see ffMOL.itp, MOL.itp and mol_gmx.pdb files which are converted into hybrid files. Thank you very much for your help.
Yes, it is compatible, but you first need to convert topologies from charmm format to gromacs. This can be achieved with charmm2gmx GitHub - Lemkul-Lab/cgenff_charmm2gmx: Python scripts to convert CGenFF stream files to GROMACS format
1 Like
Thank you very much for the quick response. I can see that I get one itp file which can be separated into 2 file MOL.itp and ffMOL.itp. But I am no sure what to do with prm file. Should I put these in the folder as well? OR prm file has nothing to do with PMX? Thank you very much.
prm contains ff parameters. You need to fill them into MOL.itp. For that you can use script fill_cgenff_itp.py in src/pmx/scripts
1 Like