[gmx-users] CHARMM force file error in gromacs

[Mark Abraham]

Hi,

The list cannot accept attachments. What did you to try to understand why
the pair of files that you think match do not match for the program?

Mark

On Tue, 18 Jul 2017 09:19 Vikram Dalal <vikra.pbt2015 at iitr.ac.in> wrote:

> 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
> --
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