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

[Justin A. Lemkul]

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

-- 
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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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