[gmx-users] conversion issue from .str to .itp

[Justin Lemkul]

On 6/15/18 10:39 AM, abhisek Mondal wrote:
> Hi,
> I'm facing an issue converting nap.str into nap.itp.
> I used nap.mol2 file in CGenFF server to get the nap.str file. However when
> I use the following command to convert, I get the following error:
>
> python cgenff_charmm2gmx.py NAP NAP_Hadded.mol2 nap2.str charmm36.ff
>
> Error:
> NOTE1: Code tested with python 2.7.3. Your version: 2.7.13 |Continuum
> Analytics, Inc.| (default, Dec 20 2016, 23:09:15)
> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
>
> 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  nap2.str : 3.0.1
> --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.
> Traceback (most recent call last):
>    File "cgenff_charmm2gmx.py", line 799, in <module>
>      m.read_charmm_rtp(rtplines,atomtypes)
>    File "cgenff_charmm2gmx.py", line 540, in read_charmm_rtp
>      self.G.add_node(self.natoms, atm[self.natoms])
> TypeError: add_node() takes exactly 2 arguments (3 given)

The script has problems when trying to use networkx versions in the 2.x 
series. Use version 1.11 or anything in the 1.x series. Contact me 
directly if you have issues as this is not a GROMACS problem.

-Justin

-- 
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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.thelemkullab.com

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