Dear all,
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 :
command used:
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.
Yours sincerely,
Revathi.S
M.S. Research Scholar
Computational Biophysics Lab,
Department of Biotechnology,
Indian Institute Of Technology, Madras
India
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