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

abhisek Mondal abhisek.mndl at gmail.com
Fri Jun 15 16:40:53 CEST 2018

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

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>
  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)

Help me out here.


Abhisek Mondal

*Senior Research Fellow*
*Protein Crystallography Group*

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

*Kolkata 700032*


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