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

Joern Lenz 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 
suggested, too.

However, what about using AMBER FF instead of OPLS ? Shouldn't make any 
difference, right ?



Justin A. Lemkul wrote:

    Joern Lenz wrote:

        dear gmx-users,

        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 
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 

        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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