[gmx-users] Re: help on parameterization
David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 25 23:06:22 CEST 2008
Julio Benegas wrote:
> Dear David,
> We are sorry to bother you on perhaps a simple question, but elusive to us.
> We want to run a MD simulation of three units of chitosan.
> We are using Gromacs ffG53A6 force field and we can not find in the
> corresponding library the parameters corresponding to the NH2 group in
> that type of molecule.
> Our question is if it is O.K. to use the parameterization of the NH2 group
> that appears for aminoacids.
> The question also involves keeping the glucose parameterization as it is
> in the library.
> We thank you very much for your help
Please keep questions on the list.
For GROMOS like force field most people look for similar groups. NH2
from amino acids could be a good solution.
> Dr. Julio Benegas
> Dpto Física/IMASL
> Univ. Nacional de San Luis/CONICET
> 5700- Sann Luis
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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