[gmx-users] D-amino acids simulation

Mark Abraham Mark.Abraham at anu.edu.au
Mon Feb 20 23:15:55 CET 2006

Arnold Perez Goicochea wrote:
>   Dear All,
> I am planning to perform MD simulations with some D-amino acids. I 
> normally use OPLS-AA with GROMACS 3.2.1, but I think it won't work if 
> D-amino acids  are used. The FF torsion potential would not be suitable 
> for those aminoacids.

Obviously, there's no energetic difference in the real world between L- 
and D-amino acids. Thus, the torsion potentials would only be unsuitable 
if they were designed to enforce L-chirality, but if you look at the 
functional forms it is clear that this is not the case for proper 
dihedrals so long as the reference angles in the force fields are 
multiples of pi. However if there are improper dihedrals in OPLS-AA for 
out-of-tetrahedral distortions of the alpha-C (your homework exercise! 
:-) ), then the (signed) reference angles will be L-chiral-specific. 
This sort of thing tends to come in united-atom force fields, however. 
Inverting the sign of the reference angles will be enough to fix the 
problem however. You should check if such impropers exist in OPLS-AA 
(and that proper dihedrals don't have non-pi-multiple reference angles), 
read the description of the dihedral potentials in the GROMACS manual, 
and, if necessary, tweak reference angles and compare L- and D- force 
fields on various amino acids carefully.


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