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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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