[gmx-users] cgenff_charmm2gmx.py failed

Justin Lemkul jalemkul at vt.edu
Mon May 26 01:31:02 CEST 2014

On 5/25/14, 4:23 PM, Albert wrote:
> Hello:
> I am trying to convert cgenff format file into Gromacs format by command:
> test> cgenff_charmm2gmx.py LIG LIG.mol2 LIG.str
> /home/albert/install/gromacs-4.6.5/share/gromacs/top/charmm36-mar2014.ff/

This wasn't your actual command (the output below indicates the stream file is 
named morphine.str); providing exact commands is critical to arriving at a 
solution.  It could be something very simple that is the problem that you're 
covering up here.

> However, it failed with messages:
> NOTE1: Code tested with python 2.7.3. Your version: 2.7.6 (default, Nov 21 2013,
> 15:55:38) [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  morphine.str : 2b8
> --Version of CGenFF detected in
> /home/albert/install/gromacs-4.6.5/share/gromacs/top/charmm36-mar2014.ff//forcefield.doc
> : 2b8
> 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 789, in <module>
>      m.read_charmm_rtp(rtplines,atomtypes)
>    File "/home/albert/bin/cgenff_charmm2gmx.py", line 526, 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 "Include parameters that are already in CGenFF" when generating
> the str file.

That's not relevant; it just happens to be the last thing printed to the screen 
before parsing the topology.

There's not enough information here to diagnose what's going on.  The contact 
information for the script's author (a colleague of mine) is provided in case of 
problems.  Rather than posting a non-Gromacs problem here, you should contact 
either him or me directly and provide your .mol2 and .str files.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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