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On 7/10/2011 9:18 PM, ITHAYARAJA wrote:
<blockquote
cite="mid:CA+kBMrO_xHysUvn4tJeAn2YRCO+L0vUNMO53X2Jtc1wJa+dUOw@mail.gmail.com"
type="cite">Dear Sir,<br>
<br>
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.<br>
</blockquote>
<br>
You are probably seeing an artefact of <a
href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions</a><br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CA+kBMrO_xHysUvn4tJeAn2YRCO+L0vUNMO53X2Jtc1wJa+dUOw@mail.gmail.com"
type="cite">
<br>
Please help me to get out of this problem.<br clear="all">
<br>
-- <br>
<br>
Ithayaraja M,<br>
Research Scholar,<br>
Department of Bionformatics,<br>
Bharathiar University,<br>
Coimbatore 641 046,<br>
Tamil Nadu<br>
India<br>
<br>
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</blockquote>
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