[gmx-users] lipid .gro file

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Wed Jul 19 08:39:08 CEST 2006

> I am trying to convert a pdb file containing all DMPC 
> coordinates to .gro file. I have searched through the web and 
> found out that I am not to use pdb2gmx directly and also that 
> I have to make a .top file containing dmpc.itp and lipid.itp files. 
> I am a beginner in gromacs so kindly help me as to how
> can I generate the .gro file? I have the .top file
> ready as is explained on Peter Tielemann's website.
> I think somehow I have to include the dmpc parameters
> to the residue topology database so that it recognises
> the dmpc molecules, but how to do that?

No, you don't have to do that since a .gro file is simply a coordinate
file.  Like a PDB file.  So to convert a PDB file to a .gro file, simply
use the editconf -f file1.pdb -o file2.gro

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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