Dear Sir/Madam,
I am trying to comput the DG for a drug binding to a receptor with PMF
approach.
I do the umbrella sampling for 20 windows with receptor-drug distance
restraint min distances set at 5, 6, 7, 8, 9 A. Should I extend the min
distance till the drug is totally removed from the receptor binding site?
Is it a must that all these results should be overlap? Should I include all
these windows' results to WHAM analysis?
Best regards,
Annie
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Received on Sun May 13 2007 - 06:07:41 PDT
