[gmx-users] cgenff_charmm2gmx.py failed

Albert mailmd2011 at gmail.com
Sun May 25 22:31:42 CEST 2014


I am trying to convert cgenff format file into Gromacs format by command:

test> cgenff_charmm2gmx.py LIG LIG.mol2 LIG.str 

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 
: 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>
   File "/home/albert/bin/cgenff_charmm2gmx.py", line 526, in 
     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.

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