[gmx-users] Error of CgenFF convert to itp

Justin Lemkul jalemkul at vt.edu
Tue Oct 30 02:17:14 CET 2018

On 10/28/18 11:04 PM, Mijiddorj B wrote:
> I would like to generate parameters for small molecule using CGenFF. I
> generated str file using cgenFF. However, I could not convert to itp file
> using cgenff_charmm2gmx.py because of following error:
> Please advice me.
> 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  mol.str : 4.0
> --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)

You need Python NetworkX version 1.11. The versions in the 2.x series 
are not compatible with the script.



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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