[gmx-users] Ligand scattered out of the protein

Dallas Warren Dallas.Warren at monash.edu
Sun Oct 9 23:12:02 CEST 2011

PBC issue?


Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of ITHAYARAJA
Sent: Friday, 7 October 2011 9:19 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Ligand scattered out of the protein

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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