[gmx-users] Error of CgenFF convert to itp

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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