[gmx-users] GROMOS 53A6 AND charmm36.ff
magnus at helium.biomol.uci.edu
Wed Jan 18 01:43:05 CET 2012
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
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:
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, PhD
Department of Physiology and Biophysics
University of California, Irvine
Irvine, CA 92697-4560
Fax: (949) 824-8540
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