[gmx-users] MD simulating cyclic peptides including D-aminoacids

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 15 19:28:43 CET 2009

Justin A. Lemkul wrote:
> Joern Lenz wrote:
>> dear gmx-users,
>> i want to do MD simulations of cyclic-peptides that include D-aminoacids.
>> I work with GROMACS 3.3.1 and want to use the AMBER FF ports.
>> Is it possible to simulate D-aminoacids without defining anything else ?
> Not likely, unless someone has developed the parameters already.  Within 
> the ffamber ports, I believe all of the amino acids are in their 
> standard L configuration.
>> Will the torsions make problems or do I have to define somthing new ?
> My guess is that any D-amino acids would be converted to L upon energy 
> minimization, if the energy barrier can be overcome without atomic 
> collision.

I'm not sure. We have successfully simulated D-amino acids with OPLS 
(e.g. Int. J. Mass. Spectrom. 248 (2006) p. 124). If the coordinates are 
in the D-conformation I don't see why they should change, unless there 
is an improper dihedral on them. Please try some GLy-X-Gly peptides to 
test it.
>> What do I have to take care about ?
> Well, that's for you to decide in designing your project :)
> -Justin
>> Any help is much appreciated.
>> Greetings,
>> Joern
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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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