On 7/10/2011 9:18 PM, ITHAYARAJA wrote:
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.
You are probably seeing an artefact of
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
Please help me to get out of this problem.
--
Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
India
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