after running
python3 cgenff_charmm2gmx_py3_nx2.py LIG lig_fix.mol2 lig.str charmm36-jul2020.ff
I am getting following error:
error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (44) and top (0) are unequal
Usually this means the specified residue name does not match between str and mol2 files.
Can anybody help me out with the above problem?
Do you need to use the Charmm force field? If you can use AMBER force fields, I recommend my LiGRO program:
https://www.ufrgs.br/lasomfarmacia/node/7?language=en
Your ligand file is not prepared as per the standard pdb file. Check once again. Still facing the error send the ligand and protein file.
I think you would need to update your molecule topology file, as you might have missed it at some particular step. If the entries in the coordinate file do not match the topology file, GROMACS usually returns errors.
I do not know the exact command to do this in python but you can check it out
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