[gmx-users] how to run charmm2gromacs-pvm.py correctly?

Albert mailmd2011 at gmail.com
Wed Nov 28 10:13:09 CET 2012

On 11/27/2012 07:43 PM, David van der Spoel wrote:
> On 2012-11-27 17:58, Albert wrote:
>> Hello:
>> I am trying to convert the output from CGenFF website into Gromacs .itp
>> format by command:
>> python charmm2gromacs-pvm.py charmm.rst
> you need an extra file. IIRC the cgenff method gives you two files. 


  thanks for kind reply.

  In fact we get only one .str file from CGENFF server, and we have to 
split them into two files manually:

     In top_ligand.rtf (topology file): copy the lines between read rtf 
card append and the next END (both excluded). Manually modify the line 
starting with RESI in order to set your chosen residue name. This will 
be the name of the residue in the PDB file.
     In par_ligand.inp (parameter file): copy the lines between read 
param card flex append and the next END (both excluded).

Now I generate the above two files and put them into the folder 
cgenff.ff, and run command:

./charmm2gromacs-pvm.py cgenff.ff

but it still claimed:

Traceback (most recent call last):
   File "./charmm2gromacs-pvm.py", line 33, in <module>
     parFile = open(sys.argv[2], 'r')
IndexError: list index out of range

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