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From: Richard Daigle (richard.daigle.3_at_ulaval.ca)
Date: Mon May 04 2009 - 12:21:41 CDT
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Dear all,
I am writing you because I am unable to reproduce NO/O2 solvation energies by
implicit ligand sampling.
I am getting 1.34 kcal/mol and 1.72 kcal/mol for NO and O2, respectively. In,
the orignal paper, solvations energies of 1.60 kcal/mol and 1.97 kcal/mol
were reported for NO and O2.
For this calculation, I believe that I did correctly the same procedure as
published in the original paper of Cohen and al. (Biophys. J. 2006, 91,
1844-1857). Briefly, I performed implicit ligand sampling (NO and O2) of a 5
ns trajectory of a water box (40Å x 40Å x 40Å). PMF of each grid point was
converted to its associated occupancy probability ( e^(-PMF) ) using volutil.
Then, occupation probabilities were averaged over all grid points and the
solvation free energy was calculated according to the formula :
deltaG = -RT ln(computed average)
Here is the volmap command I used :
volmap ligand [atomselect $molid "segname WAT"] -allframes -combine
pmf -minmax {{ -8 -8 -8 } { 8 8 8 }} -dx "./box_$job.dx" -dihetero -conf
50 -probe1 -0.20 1.85 -probe2 -0.12 1.70 -bond 1.15 -cutoff 12 -subres 2
Help will be very appreciated !
Thank you !
Richard Daigle
Étudiant au doctorat en biochimie
Laboratoire du professeur Patrick Lagüe
Université Laval, PROTEO
Québec, Canada
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