[gmx-users] CgenFF conversion failed

[Justin Lemkul]

On 11/19/17 11:34 AM, Albert wrote:
> Hello,
>
> I generated a ligand.str file from Parachem website. Then, I try to 
> convert it to Gromacs format with command line:
>
> >cgenff_charmm2gmx.py UNK ligand.mol2 ligand.str charmm36-jul2017.ff
>
>
> However, the job always failed with the following messages:
>
> NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, 
> Jul 01 2016, 15:36:53) [GCC]
>
> 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  ligand.str : 4.0
> --Version of CGenFF detected in charmm36-jul2017.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 "/home/albert/bin/cgenff_charmm2gmx.py", line 799, in <module>
>     m.read_charmm_rtp(rtplines,atomtypes)
>   File "/home/albert/bin/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)
>
>
> I didn't select the 'Include parameters that are already in CGenFF' 
> option when uploading a molecule into CGenFF.
>

That's not relevant to this error.

>
> Does anybody have any idea how to solve this problem?
>

I have had this problem reported to me several times, yet I have never 
been able to reproduce it. I am beginning to suspect a bug in networkx 
or some weird versioning issue. If you send me your files (.str and 
.mol2) off-list, I will look at it, but unless I am able to reproduce 
the issue, there's not going to be anything I can do.

-Justin

-- 
==================================================

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

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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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