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 Mon May 12 2014 - 05:00:04 PDT
