[gmx-users] conversion of str to itp

[abhisek Mondal]

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 unequalUsually this means the specified
residue name does not match between str and mol2 files*
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.

-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*