[gmx-users] D-aminoacids

Andreas Kukol A.Kukol at warwick.ac.uk
Mon Oct 4 15:20:32 CEST 2004

Dear all,

If I want to use a D-amino acid residue as opposed to the natural L-aminoacid is it correct to modify the improper dihedral in the .top file created by pdb2gmx, by specifiying the improper dihedral as -35.364 degrees:

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3
    4     1    20     6     2          -35.364  (<-- I added this number only)
(  CA   N     C    CB   <-- atom names for clarification)

Is it correct that when using the GROMACS all hydrogen forcefield, I don't need to change anything, as long as the starting structure has the correct stereochemistry ?

Intersting is, that even with the 'all hydrogen' forcefield the impoper dihedral shown above is generated.

I would be grateful for any confirmation/clarification.
Many thanks


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