VMD-L Mailing List

From: Richard Daigle (richard.daigle.3_at_ulaval.ca)
Date: Mon May 04 2009 - 14:06:22 CDT

I am using version 1.8.6 (April 6, 2007)

Thank you !

Richard Daigle

On Monday 04 May 2009 14:49:44 John Stone wrote:
> 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 

-- 
Richard Daigle
Étudiant au doctorat en biochimie
Laboratoire du professeur Patrick Lagüe
Université Laval, PROTEO/CREFSIP
Québec, Canada