[gmx-users] protein and ligand is not forming complex after completing simulation

[Justin Lemkul]

On 7/27/16 7:31 AM, Swagata Patra wrote:
> hi everyone,
>
> I  simulated protein-ligand complex for 30ns and then visualize the complex
> after simulation in pymol.
>
> I got the .pdb file using two commands from final simulated file.
> One is using trjconv, from .xtc to .pdb. When I am visualizing this .pdb
> file, protein and ligand has not formed any complex.
> Another one is using editconf, from .gro to .pdb. When I am visualizing
> this .pdb file, protein and ligand  formed  complex.
>
> Why is this happening? Can anyone explain it?
>

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

Dealing with complex systems requires complex use of trjconv.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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