[gmx-users] Ligand scattered out of the protein

[Mark Abraham]

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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