[Apbs-users] stability and program collapse

[Dimitrios S. <dim...@gm...>]

Dear APBS users,

Some authors (Suenaga et al., *J Biol Chem*, 2004,  Adekoya et al., *J
Struct Biol*, 2006, Ganoth et al., *Biophys J*, 2006, Zeng et al., *J Phys
Chem B*, 2008, Moroy et al., *JBC*, 2009 is just a brief list of their
works) would perform the MM/PBSA calculations only after structural
convergence (in terms of RMSD) is achieved.
Some other authors wait for the "effective energy" (Huo et al., *J Comp Chem
* , 2001) or in general for energetic values (Laitinen et al., *Org Biomol
Chem*, 2003, Xu and Wang, *PROTEINS*, 2006) to be converged. Should one
perform the MM/PBSA calculations on well-converged portions of simulations
only? And if so, what should one monitor to be converged (structural
features, energetical values, or both)?
In case the protein undergoes massive conformational changes which are
limited to the N- and C-terminal ends (this is my case) is it possible to
"cut" the highly mobile parts of the protein and perform all of my
calculations (both the molecular mechanics and APBS-mediated) on the
terminal-less structures assuming that the contributions are equal for the
different investigations?
 Any suggestion is more than welcome!!!

I have another methodological question. In some cases, my APBS process dies
very early: is it possible that this is due to the fact that I'm requesting
a very high resolution? My values in one of these cases are

coarse grid dimensions: 90.051 x 81.970 x 70.389
fine grid dimensions:      68.051 x 59.970 x 48.389
grid points:                      385   x   353   x   289

Thank you very much in advance!

d.

_________________________________________________________________________________________________
Dulbecco Telethon Institute c/o DIBIT Scientific Institute
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