[gmx-users] conversion of str to itp

[abhisek Mondal]

Thanks a lot for the support...
Solved it !

On Mon, Feb 19, 2018 at 6:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
>
> -Justin
>
> Location of files:
>> https://drive.google.com/drive/folders/0B6O-L5Y7BiGJfmQ4N2Fp
>> blBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU?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
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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-- 
Abhisek Mondal

*Senior Research Fellow*

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

*Kolkata 700032*

*INDIA*