AMBER Archive (2001)

Subject: Re: MM-PGBSA Question!!

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Sat Dec 22 2001 - 08:46:53 CST

Hello Bernd,
I can try to answer only your first question:

The large fluctuations of energies among snapshots are the reality, I rather
wonder how the energies (e.g. interaction
energies differing by a couple of kcal/mol) can come out with qualitative
precision. The small deviations you can
sometimes see in the literature are "block" deviations, i.e. average of the
values of the 1st and 2nd half of production run.

Hope this helps,

  Martin Lepsik

> 1.)We performed several mm-pbsa calculations of DNA and
> although two simulations starting from different
> conformations exhibit a similar mean value (+- 1kcal/mol)
> of the free energy
> the standard deviations are extremly large (about 20 kcal/mol).
> The standard deviations of similar calculations (Srinivasan et al. 1998 )
> is much smaller while Wu et al. 2002 had comparable standard
> deviations. Does anyone have an idea why this happens, and is the
> calculation of small (about 10 kcal/mol) delta G still allowed.
>
> 2.) Wang et al. (2001) performed a normal mode analysis of a large
> protein and due to the size only the residues within 12 A of interest
> were used for the normal mode calculation. Does anyone know how they
> did this. Did they use ibelly for the other residues or did they cut out
> the part
> of interest.
>
> Thanks in advance Bernd Wellenzohn