Hi,
and thanks, David and Justin, for your answers.
I thought there might be a problem with the dihedral angles like David
suggested, too.
However, what about using AMBER FF instead of OPLS ? Shouldn't make any
difference, right ?
Greetings,
Joern
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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