[gmx-users] D-Ala topology for OPLSAA

Erik Lindahl lindahl at stanford.edu
Wed Feb 5 00:08:05 CET 2003

On Tuesday, Feb 4, 2003, at 13:18 US/Pacific, Attila Borics wrote:

> Hi!
> I try to simulate a peptide containing D-Ala.
> I couldn't find this residue in OPLSAA's residue topology,
> and since chirality is not defined by impropers as it is in GROMOS96,
> I'm a bit confused what should I use. Define an additional improper for
> the residue ALA, and insert it to .rtp as DALA, or try to manipulate
> with the dihedrals? If someone had this problem before please help me.
> Maybe someone already created a residue topology for D-Ala in OPLSAA.
> I would appreciate any help.
> Thanks
> Attila

Hi Attila,

You don't need a special residue topology - if the coordinates are in 
the D state
when you start, the hydrogens will prevent it from flipping over to L. 
(just as nature does it)



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