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.scripps.edu on behalf of Ray Luo
Sent: Mon 3/17/2008 1:33 PM
To: amber.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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Received on Fri Apr 18 2008 - 21:11:48 PDT
