Dear APBS users,

Some authors (Suenaga et al., J Biol Chem, 2004
Adekoya et al., J Struct Biol, 2006Ganoth 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!


Dulbecco Telethon Institute c/o DIBIT Scientific Institute
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