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

From: Catein Catherine <askamber23.hotmail.com>
Date: Sun, 19 Jun 2011 12:55:37 +0800

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,
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Received on Sat Jun 18 2011 - 22:00:03 PDT
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