[gmx-users] cgenff_charmm2gmx.py failed

[Gurunath Katagi]

Hi ..
from the message u have put, looks like there is a mismatch between the
python version that u r using and the version of python used by cgenff.
Can u install  python 2.7.3 and try... ?

thank you
Gurunath


On Mon, May 26, 2014 at 1:53 AM, Albert <mailmd2011 at gmail.com> 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/
>
>
> 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.
>
>
> thank you very much.
> Albert
>
>
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