[gmx-users] CHARMM force file error in gromacs
vikra.pbt2015 at iitr.ac.in
Tue Jul 18 09:19:15 CEST 2017
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,
Department of Biotechnology
Indian Institute of Technology, Roorkee
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