[AMBER] Any recommendations regarding IGB parameter in Normal Mode section of mm_pbsa analyses ?

From: Marek Maly <marek.maly.ujep.cz>
Date: Sun, 30 Jan 2011 21:51:30 +0100

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,


Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
AMBER mailing list
Received on Sun Jan 30 2011 - 13:30:05 PST
Custom Search