Thanks, Jason!
It's not clear for me why the value of EGB so different in both complexes
although the same ligand have been used in those systems. In that example
EEL might be different because of difference in the electrostatic
environment within the both proteins but EGB (the masking of the ligand
from the polar solvent) should be the same for the same ligand shouldn't it?
James
2014-05-12 15:52 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Sun, 2014-05-11 at 11:43 +0400, James Starlight wrote:
> > Dear Amber users!
> >
> [snip]
> >
> > These results suggests that (i) relative affinity (which corresponds to
> the
> > tightness of the complex and its time-life) should be higher in case of
> > complex 2 (lover dG) and (ii) the gain in dG in the second case is cased
> by
> > the lover entropy penalty (-20 vs -23 kccal/mol) having the same dH
> values
> > for both complexes. Are these suggestions correct?
>
> There seems to be roughly equivalent contributions from the GB energy
> differences and the quasi-harmonic entropy differences (the entropy
> differences are a little larger, but the results are too close to
> distinguish in my opinion).
>
> > (iii) On what output details should I paid begger attention if I'd like
> to
> > define which term (e.g electrostatic or hydrophobic ) has largest
> > contribution to the dH ? E.g from those outputs I've noticed the same dH
> > for both complexes but big deference in values of EEL and EGB for both
> > complexes. For instance taking complex 2 does the lover EEL indicate on
> > stronger electrostatic forces between protein and ligand and the higher
> EGB
> > point on the higher desolvation penalty (masking polar ligand from the
> > polar solvent) ?
>
> Seems to be a reasonable conclusion.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Wed May 14 2014 - 03:00:03 PDT
