As far as I know, there's no lipid force field in Amber (yet, it's being
worked on), so I would say that the parameters necessary to build
cholesterol and the succinate do not exist, and I would doubt gaff's ability
to deal with such large lipid molecules. GAFF was designed to deal with
small organic ligands, and cholesterol is bordering on a large system.
My suggestion would be to look through the literature to see how other
people ran simulations with cholesterol or related compounds.
Another thing -- there is also a program, chamber, that will convert a
CHARMM psf into an Amber prmtop so you can run the CHARMM force field in
sander or pmemd, and CHARMM *does* have a lipid force field AFAIK. YOu
would just have to build your Lipid system in CHARMM first.
HTH,
Jason
On Wed, Aug 10, 2011 at 2:43 PM, TAEJIN KIM <liquidhelium4k.yahoo.com>wrote:
> Dear Amber Users
>
> I am preparing MD simulations of cholesterol and cholesteryl hemisuccinate.
> Does Amber have topology (prep) and appropriate force fields for these
> molecules?
> If Amber does not have them, is general Amber force field (GAFF) good
> enough for these molecules?
> Thank you.
>
>
> TJ
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Aug 10 2011 - 15:30:04 PDT
