AMBER Archive (2002)

Subject: MM-PGBSA Question!!

From: Bernd Wellenzohn (Bernd.Wellenzohn_at_uibk.ac.at)
Date: Tue Oct 22 2002 - 07:46:29 CDT

Dear Amber users!!

I have two questions regarding mm-pbsa.

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