[gmx-users] GROMOS 53A6 AND charmm36.ff

Magnus Andersson magnus at helium.biomol.uci.edu
Wed Jan 18 01:43:05 CET 2012

Hi all,

I want to use the GROMOS 53A6 forcefield for the protein, water, ions. For the membrane I intend to use charmm36.ff. 

I downloaded the charmm36.ff and put the folder as a sub-folder in /sw/share/gromacs/top/ as suggested in the GROMACS manual.

When I go:

pdb2gmx -f test.pdb -o -p -i -ignh -ff charmm

I get:

Fatal error:
Library file ffcharmm.ff.rtp not found in current dir nor in default directories.

So, I renamed "lipids.rtp" in the charmm36.ff folder to "fflipids.rtp" and moved the file into /sw/share/gromacs/top/

and now I get around that issue, but get a new error message:

Fatal error:
Library file fflipids.atp not found in current dir nor in default directories.

And it's not obvious to me which of the files in the charmm36.ff folder this corresponds to?

I guess my question is how to use pdb2gmx with he GROMOS 53A6 forcefield AND the charmm36.ff forcefield?

Best regards /

Magnus Andersson

Magnus Andersson, PhD
Department of Physiology and Biophysics
University of California, Irvine
Irvine, CA 92697-4560
(949) 824-6993
Fax: (949) 824-8540

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