[gmx-users] conversion of str to itp

Justin Lemkul jalemkul at vt.edu
Mon Feb 19 13:57:33 CET 2018

On 2/19/18 7:26 AM, abhisek Mondal wrote:
> Hi,
> I have generated a .str file from .pdb file using CGenFF server. But
> whenever I try to convert the .str file to gromacs specific topology using:
>   *python cgenff_charmm2gmx.py NAP nap.mol2 nap.str charmm36.ff*
> I'm getting the following error:
> *NOTE1: Code tested with python 2.7.3. Your version: 2.7.13 | packaged by
> conda-forge | (default, May  2 2017, 12:48:11) [GCC 4.8.2 20140120 (Red Hat
> 4.8.2-15)]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  nap.str : 3.0.1--Version of CGenFF detected in
> charmm36.ff/forcefield.doc : 4.0WARNING: CGenFF versions are not
> equivalent!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 (73) and top (0) are unequal

Your answer is right here:
> Usually this means the specified
> residue name does not match between str and mol2 files*

Look in nap.str and you will find "RESI /scrat" so the script clearly 
finds nothing called "NAP" in the stream file and therefore fails. 
Rename the residue appropriately and it will work.

If you have further problems with this conversion, contact me directly. 
This is not a GROMACS problem.


> Location of files:
> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU?usp=sharing
> I do not understand. Is this all happening because of the version conflict
> of CGenFF ? If it is so then please suggest me how can I make it work in
> gromacs.
> Thank you.


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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