AMBER Archive (2009)

Subject: [AMBER] how to use amber to verify the reason for difference in affinity

From: Josmar R. da Rocha (
Date: Tue Nov 24 2009 - 16:01:34 CST

Dear amber users,

I would appreciate if someone could give a tip or to point some reference on how to use amber in my problem. I tested two very similar compounds against a protein and one of then is 500-fold more potent than the other. I guess that the diference is caused mainly due to a charge stabilization of a deprotonate cystein through the interaction with a diene fragment, which is replaced by a saturated fragment in the less potent compound.

1-How could I verify this hypothesis?
2-When I use MM, is this kind of effect is taken into account?

Thanks in advance

Josmar Rocha

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