[gmx-users] CHARMM force file error in gromacs

[Vikram Dalal]

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:- 

 http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs



 
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,
VIKRAM DALAL
Research Scholar
Department of Biotechnology
Indian Institute of Technology, Roorkee
INDIA