[gmx-users] Ligand scattered out of the protein

ITHAYARAJA ithayaraja at gmail.com
Fri Oct 7 12:18:52 CEST 2011

Dear Sir,

I am doing simulation work with protein-ligand complex (3 ligands). I
modeled the protein using modeller, their ligand (two) was translated from
the template and one them were docked by autodock 4.2. The protein and
ligand coordinates were generated as described by the manual. the ligand
particles were scattered out of the pocket when I was doing configuration
(editconf -bt triclinic -f trp1.pdb -o trp2.pdb -d 0.85). I was using
GROMOS96 43a1 force field.

Please help me to get out of this problem.

Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
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