VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 04 2009 - 13:49:44 CDT

Richard,
  The ILS code in VMD has been changed significantly over the last
several weeks, and this may (or may not) be related to the differences
you're seeing. Which version of VMD were you running for these
calculations?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 04, 2009 at 01:21:41PM -0400, Richard Daigle wrote:
> 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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