anthony.costa at gmail.com
Fri Sep 24 15:39:56 CEST 2010
On Fri, Sep 24, 2010 at 03:28, Stefano Pieraccini
<Stefano.Pieraccini at unimi.it> wrote:
> I would like to use gromacs to simulate a peptide containing a D-proline
> using the opls force field. I guess that, considering that L- and D- PRO
> differs only for chirality, the two a.a. topologies should little differ,
> and that an improper torsion and/or torsional terms should be modified in
> D-PRO topology with respect to L-PRO, but I am not sure on how to modify the
> improper torsion ( it is _C CA N CD in L-pro) and if it is correct to do so
> or only torsional terms should be modified.
As long as you're using an all-atom forcefield (OPLS, so I assume you
are) there is no reason to need to change any part of your topology.
Simply starting with the correct configuration is perfectly
sufficient. Otherwise though, for UA forcefields, there is no hydrogen
and therefore no configurational constraint. I remember a few
discussions on the mailing list about this issue, I think some from me
a few years ago.
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