Hello all,
As I see also the mm_pbsa analysis was improved in Amber11 and some new
choices were implemented.
My particular question is: Are there any recommendations regarding the
value of IGB parameter in Normal Mode analysis section of
input file for mm_pbsa.pl analysis ? I mean, it is better (to obtain more
reliable results) to use GB model (IGB=1) or a
distance-dependent dielectric (IGB=0) here if one would like to obtain TdS
contribution of receptor/ligand complexation
simulated in explicit TIP3P water ?
Maybe that the answer is dependent on given simulated/analysed system. In
this case It is at least possible
to provide some general characterization of systems for which is better to
use IGB=0 and those for which
IGB=1 might be more appropriate ?
Thanks in advance for any comments/personal experience !
Best wishes,
Marek
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Received on Sun Jan 30 2011 - 13:30:05 PST
