[gmx-users] MD simulating cyclic peptides including D-aminoacids
JLenz at zbh.uni-hamburg.de
Wed Jan 21 13:54:41 CET 2009
and thanks, David and Justin, for your answers.
I thought there might be a problem with the dihedral angles like David
However, what about using AMBER FF instead of OPLS ? Shouldn't make any
difference, right ?
Justin A. Lemkul wrote:
Joern Lenz wrote:
i want to do MD simulations of cyclic-peptides that include
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
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
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 :)
Any help is much appreciated.
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