Hi,
I am running mm/pbsa (using delphi for PB) on two systems with the same kinase receptor and two chiral compounds(isomers). The starting coordinates of receptors before MD simulation are the same. The receptor uses Amber94 charge and compounds uses gasteigar charges. The results are a little surprise to me since the PBCAL values for the same receptor in those two systems( through separate MD and mm/pbsa) have about 40 Kcal difference(std=22), and the ligand also has 1.5 difference(std=1). What could be the possible reasons to make the PB values of two exactly same receptors so different?
Does MD cause this since half of residues could move during MD? Is it reasonable to let less residues move during MD (< 25% total residues) since my receptor is from crystal structures though it doesn't has ligand in it.
Any suggestions will be highly appreciated! Thanks in advance.
Nan
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Received on Tue Jun 29 2004 - 20:53:00 PDT
