Hi everyone,
I have to do molecular dynamics simulation of a zinc containing protein.
I have kept the Zn molecule along with the protein and generate the topology file by using CHARMM36 force field in Gromacs5.1.4.
I have converted the ligand PDB file into mol2 by discovery studio visualizer. I have submitted this mol2 on CGenFF and get the str file.
But I got the -2.0 charge on my ligand in str file.
Then I kept this str file, mol2 file, cgenff_charmm2gmx.py and charmm36-jul2017.ff in same directory.
I ran the "python cgenff_charmm2gmx.py" from the terminal of same directory.
I got this message:-
Usage: RESNAME drug.mol2 drug.str charmm36.ff
I have attached here my mol2, str, cgenff_charmm2gmx.py and charmm36-jul2017.ff.tgz.
Thank you in advance.
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