Dear AMBER users,
I am using AMBERTOOL14 for our MD
simulation. Initially I prepared topology and coordinate file for
ligand, receptor, and complex separately( for MM-PBSA calculation).
After that, i added solvatebox at the distance of 9 Angstrom. Again i
prepared, topology and coordinates for solvated complex and save as
pdb file. I viewed pdb file Chimera. Here, the ligand molecule had
broken and the connectivity was missing completely. we can't use this
topology and coordinate file for our calculation. Please give your
valuable suggestion, to find out the problem.
Thank you,
--
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M.SIVANANDAM
Research Scholar
Department of Physics
School of Physical Sciences
Periyar University
Salem-636 011
Mobile- 9965582730, 9042066076
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Received on Thu Apr 14 2016 - 00:30:03 PDT
