[gmx-users] CHARMM force file error in gromacs

Vikram Dalal vikra.pbt2015 at iitr.ac.in
Tue Jul 18 09:19:15 CEST 2017

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 downloaded the CHARMM36 force field from this link:- 


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" PDC pdc.mol2 pdc.str charmm36-ff from the terminal of same directory.
I got this message:-

NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, Nov 19 2016, 06:48:10) 

[GCC 5.4.0 20160609]

NOTE2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation:

--Version of CGenFF detected in pdc.str : 4.0

--Version of CGenFF detected in charmm36.ff//forcefield.doc : 4.0

NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF.

Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (17) and top (15) are unequal

Usually this means the specified residue name does not match between str and mol2 files

I have attached here my mol2, str, cgenff_charmm2gmx.py and charmm36-jul2017.ff.tgz.

Thank you in advance. 

Thanks & Regards,
Research Scholar
Department of Biotechnology
Indian Institute of Technology, Roorkee

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