Re: AMBER: neb for path between binding sites

From: Holly Freedman <>
Date: Tue, 9 Oct 2007 17:37:20 -0600

> Hi Carlos,
> Thank you for your answer. There shouldn't be big differences in protein structure between the
> initial and final states because to get the final state I just repositioned the drug at a different position
> on the protein from where it is in the initial state and ran a few hundred steps of minimization with a
> restraint on much of the system. I think my problem is that unfornutately the elastic forces are
> causing Van Der Waals overlap between the images.

Sorry, I menat that the forces are causing Van Der Waals overlap betwen the drug and the protein within
individual images.
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Received on Wed Oct 10 2007 - 06:07:58 PDT
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