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

Joern Lenz JLenz at zbh.uni-hamburg.de
Thu Jan 15 17:47:50 CET 2009

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 ?
Will the torsions make problems or do I have to define somthing new ?
What do I have to take care about ?

Any help is much appreciated.



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