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

[David van der Spoel]

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.



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


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se