[AMBER] MMPBSA in case of highly water accessible molecules ?

From: Marek Maly <marek.maly.ujep.cz>
Date: Tue, 09 Mar 2010 22:43:11 +0100

  Dear all,

  I am just curious if the highly reccommended value of INDI constant (and
  so also the value of constant DIELC from the MM part) 1,
  is ideal also in case of interaction of two molecules which interior is
  nicely accessible to water molecules.

  I am asking because I have experienced some small positive values of dG
  (4.91, 2.48) in case of nicely complexated singlestrand
  DNA and small dendrimer (please see atached file) which interior is
  almost fully accessible for water molecules.

  Although dH was negative in agreement with evident complexation,
  positive entropic penalty -TdS more than compensated
  enthalpic gain.

  I tried to increase INDI ( and so also DIELC values 2,3 - 7) and I got
  nice improvement (more negative values dH) with
  saturation of dH around INDI = 6.

  But of course I would like to prevent me from the experiments which
  might be in contradiction with theory.
  In this case would be for me better to stay with INDI=1 and explain
  small positive values of dG as the result
  of inaccuracy of the methodology (especially in case of normal mode

  I have to say that I tried both, single and three trajectory approach
  with the similar behaviour.

  I think that my statistic is pretty good (analyses (including entropy)
  of 400 frames from the last 4ns of 14ns simulation ).

  Thanks in advance for any helpful information/advice !

     Best wishes,


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Received on Tue Mar 09 2010 - 14:00:05 PST
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