Re: [AMBER] Can I directly compare the PMF for two compounds with different size and chemical structures?

From: Carlos Simmerling <>
Date: Sun, 19 Jun 2011 06:10:46 -0400

if they are properly done, you can compare the barriers. however, both
seem very high to me.

On Sun, Jun 19, 2011 at 12:55 AM, Catein Catherine
<> wrote:
> Dear Sir/Madam,
> I have done a Potential of mean force to study the drug dissociation from a receptor.
> I wonder if I should directly compare the PMF barriers of two drugs which are significantly different in chemical structure and molecular weight.
> For example, the molecular mass of compound A = 300, and compound B = 600.
> If I found the potential of mean force barriers of compound A (50 kcal/mol) is two fold higher than that of compound B (30 kcal/mol). Given convergency and effect of window size or sample time have been checked.
> Can I conclude that the barrier of compound A dissociate from the receptor is higher than that of compound B?  Does the size or chemical structures taken into account?
> Best regards,
> Catherine
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Received on Sun Jun 19 2011 - 03:30:03 PDT
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