AMBER Archive (2002)

Subject: Re: MM-PBSA tutorial

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Mon Oct 14 2002 - 02:14:47 CDT

Dear Giulio,
by mistake a wrong value of SURFOFF was used in the examples. The value to
use for the calculation of SASA
with PB should be 0.92 (see e.g. Sitkoff et al., 94), not 0.092. Maybe
that's why your results differ.......

All the best,

 Martin Lepsik

> Hi Giulio,
>
> > I run the 02_MMPBSA_Stability tutorial of MM_PBSA in the amber7
> > distribution,
> > using Delphi 4.1
> > I found, on average, that the corrected reaction field energy is 10Kt
> > lower
> > than what reported in the ras_raf_II_wt_statistics.out.save file.
> > Did anybody else noticed a difference? Has the tutorial been run with a
> > different
> > version of Delphi?...
>
> I used the Delphi version as of May 98 ("Delphi II") to calculate the
> values in the example directory.
>
> Best regards
>
> Holger
>
> --
> +++++++++++++++++++++++++++++++++++++++++++++
> Dr. Holger Gohlke
> Dept. of Molecular Biology, TPC15
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> La Jolla CA 92037 USA
> phone: +1-858-784-9788
> fax: +1-858-784-8896
> email: gohlke_at_scripps.edu
> +++++++++++++++++++++++++++++++++++++++++++++