[gmx-users] How to process D-amino acid peptide?

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 20 09:57:04 CET 2013

On 2013-12-20 07:23, hummingbird wrote:
> I am doing a simulation of a system including a peptide made up of 36 D-amino
> acid residues. I am a new user and have no idea how to process D-amino acid.
> When I try pdb2gmx, all residues are changed to L-type in the output GRO
> file.
> Could anybody help?
> Thanks so much.
Are you sure? The only difference between L and D is the conformation, 
right? I don't think pdb2gmx changes the conformation.
> --
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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