Magnus Andersson wrote:
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.
It seems like you're using an old (pre-4.5) version of Gromacs. The force field
organization is completely different, so what you're trying to do won't work
unless you upgrade to a new version.
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?
You can't. The functional forms, representations of atoms, combination rules,
etc. are different. Even if you could somehow hack the force fields together to
make it "work," I would suspect any reviewer would immediately throw out the
results in the absence of some pretty impressive demonstration that what you're
trying to do will actually give a reasonable physical model.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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