AMBER Archive (2008)

Subject: RE: AMBER: mm_pbsa positive ELE

From: Qi Yan (kid1412_at_uab.edu)
Date: Mon Mar 17 2008 - 14:23:52 CDT

Hi,Ray:

Thank you for your response. If it is like you said, what I can do? Does
it mean I can not use mm_pbsa to calculate binding affinity?

Thnaks,

Qi

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of Ray Luo
Sent: Mon 3/17/2008 1:33 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: mm_pbsa positive ELE
 
Qi,

If you happen to have a situation where ligand binding causes the
burial of a charge, then you may have a positive electrostatic
contribution to binding free energy, i.e. desolvation of charge is
not favorable.

All the best,
Ray

On Mar 17, 2008, at 11:20 AM, Qi Yan wrote:

> Hi,all
>
> I'm trying to calculate the binding affinity of a complex and its
> mutants (I got three mutants. Each of them just change some residue
> types which are in biding site). For these mutants, the results of
> mm_pbsa seem reasonable, but, for the wild complex, the final ELE
> value is positive (final ELE = com-rec-lig). Actually, these ELE
> values of individual complex, receptor and ligand look normal. I
> don't know whether the non-zero net charge can influence the
> results. I choose "Dielectricity constant = 2.0" for all cases.
> Does anybody can point me out?
>
> Thanks in advance,
>
> Qi Yan
>

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