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.
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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