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