PBC issue? http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@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-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of ITHAYARAJA Sent: Friday, 7 October 2011 9:19 PM To: gmx-users@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 India
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