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

Erik Lindahl erik.lindahl at scilifelab.se
Fri Dec 20 10:14:28 CET 2013

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.



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
> -- 
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list