[gmx-developers] AMBER: improper dihedral for TRP

Igor Leontyev ileontyev at ucdavis.edu
Fri Apr 8 05:05:25 CEST 2011

Dihedral energy terms calculated for the same protein structure with Sorin's 
port of amber and gmx4.5.4 port are notably different. The main 
contradiction appears in TRP residues. In original AMBER force field and 
Sorin's port the last improper dihedral for TRP is defined as
"CD1   CD2    CG    CB"

while in gromacs4.5.4 amberXX.ff/aminoacids.rtp it is
"CD1    CG    CB   CD2".

Turning them back to "CD1   CD2    CG    CB" for TRP, CTRP and NTRP residues 
solves the problem.

Igor Leontyev

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