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

[Erik Lindahl]

pdb2gmx adds hydrogens if they are not present, which will be done in the L-form. If you already have hydrogens you should be able to maintain the residues in D-form.

Cheers,

Erik


On 20 Dec 2013, at 09:56, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> 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.
>> 
>> 
>> --
>> View this message in context: http://gromacs.5086.x6.nabble.com/How-to-process-D-amino-acid-peptide-tp5013440.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>> 
> 
> 
> -- 
> 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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