AMBER Archive (2008)

Subject: Re: AMBER: nmode "Atom out of bounds" for min of multiple ligands

From: David A. Case (case_at_scripps.edu)
Date: Thu May 08 2008 - 15:49:31 CDT

On Thu, May 08, 2008, Seth Lilavivat wrote:
>
> Thanks for taking a look. There is no overlap and the structure isn't bad.
> Remember I am not minimizing DNA but just 3 intercalators by themselves.
> They are positively charged so my guess is that they fly apart due to charge
> repulsion.

It is not clear that there is any simple recipe here. You could get the modes
(and thermochemistry) of each ligand molecule by itself. That would not
include any ligand-ligand interaction energy. But I think you have more
problems than this: when the time comes to evaluate the free energy of binding
(under your original scheme) you would essentially be looking at a fourth
order reaction ( DNA + 3intercaltors -> complex). And I am not sure what you
would do with such an interaction energy even if you were able to calculate
it. You probably need to think of this as three successive bi-molecular
events, and work that way.

...good luck...dac

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