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

Albert mailmd2011 at gmail.com
Tue Nov 27 17:58:58 CET 2012


I am trying to convert the output from CGenFF website into Gromacs .itp 
format by command:

python charmm2gromacs-pvm.py charmm.rst

but it said:

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

I open the script, it said:

             command line parameters:
             1            charmm topology file
             2            corresponding charmm parameter file
             3    opt        foldername, default cgenff.ff

             1            foldername/atomtypes.atp
             2            foldername/forcefield.itp
             3            foldername/forcefield.doc
             4            foldername/aminoacids.rtp
             5            foldername/ffbonded.itp
             6            foldername/ffnonbonded.itp
             7            foldername/forcefield.r2b
             8    opt        foldername/lipids.rtp    (if '!lipid 
section' statement in CHARMM top file)
             9    opt        foldername/cmap.itp        (if genCMAP = True)

It seems that the input file is a folder instead of a single file? I 
generate my ligand topology from the CGenFF website and I only get a 
.rst file....


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