AMBER Archive (2007)

Subject: Re: AMBER: PMF for DG calculation.

From: David Mobley (dmobley_at_gmail.com)
Date: Mon May 14 2007 - 09:06:46 CDT

Hi,

You may want to read some basic literature on PMFs (generally, and in
the context of binding) -- several of these questions you're asking
are really basic questions on the methodlogy and are answered very
well in a number of other places. I suspect folks on here are more
likely to be interested in helping with AMBER-related questions rather
than general methodology questions.

David

On 5/11/07, Catein Catherine <askamber23_at_hotmail.com> wrote:
> 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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