[gmx-users] charmm2gromacs.py error
revthi.sanker at yahoo.com
Mon Aug 12 20:30:01 CEST 2013
I am using your script charmm2gromacs for the conversion and I am facing certain difficulties in the same.
My doubts are:
1. In NAMD is was using CHARMM36 parameters as the parameters dor DOPC
(dioleyl phopshotidyl choline). were available in only in that.
2. For cholesteryl ester, I have used the parameters of cholesterol from
the updated version of chamm36 and added the oleate paramters from DOPC. When I imported this folder into the gromacs directory, a . gro file
corresponding to the protein and DOPC were created successfully.
3. But for the cholesteryl ester, I wanted to convert the *.rtf file and
*.prm file using your script which I am unable to :
python charmm2gromacs-pvm.py par_all36_lipid.prm top_chol_ester.rtf
It created a directory called cgenff-2b7 which I am attaching for your kind perusal.
In this directory:
aminoacids.rtp -is incomplete
atomtypes.atp,ffbonded.itp ,forcefield.doc -is empty
I also see that these correspond to charmm27 parameters. I am newbie to
simulations and gromacs and nobody else in my lab is working in this. I
will be really grateful for your support in this regard.
Thank you in advance.
M.S. Research Scholar
Computational Biophysics Lab,
Department of Biotechnology,
Indian Institute Of Technology, Madras
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