[gmx-users] cgenff_charmm2gmx.py failed

[Albert]

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