[AMBER] validation of MMPBSA results

From: Asmita Gupta <asmita4des.gmail.com>
Date: Fri, 26 Jul 2013 21:22:11 +0530

Dear users,

I have done MMPBSA analysis on a set of RNA MD trajectories. For each of
the trajectories, analysis has been done on 2000 and 17000 frames in order
to check whether number of frames have any effect on the net result. The
final DelG values that i am getting in different cases is somewhat like
this (without running nmode)

Set1: -3716.03
Set2: -4074.06
Set3: -3937.45
Set4: -3945.89 (all values for 17000 frames)

Now since each of the sets represent RNA structures with single base
substitutions, how can i verify whether the difference in the DelG values
is actually significant or not? e.g. in set1 and set3, the difference is
~200kcal/mol, is that a significant shift in the conformational free energy?

Are there any literature references available for such studies..

I also tried using MMRISM method, but it is far too time consuming for
17000 frames. The values given by PB and RISM are quite different e.g.

PB value (DelG) for set5: -3940.22
RISM (DelG) for set5: -1432.24

Why such a large difference is coming? It again raises the question of
result validity...

Thank you

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Received on Fri Jul 26 2013 - 09:00:07 PDT
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