[gmx-users] Ligand scattered out of the protein
Mark.Abraham at anu.edu.au
Sat Oct 8 04:21:00 CEST 2011
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
> 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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