[gmx-users] charmm2gromacs.py error

Revthi Sanker revthi.sanker at yahoo.com
Mon Aug 12 20:30:01 CEST 2013

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,

M.S. Research Scholar

Computational Biophysics Lab,

Department of Biotechnology,
Indian Institute Of Technology, Madras

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