[gmx-users] MD simulating cyclic peptides including D-aminoacids

[Justin A. Lemkul]

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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-- 
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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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