AMBER Archive (2007)

Subject: AMBER: PMF for DG calculation.

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Fri May 11 2007 - 21:45:30 CDT

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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