Sorry for cross posting..Can anyone answer my dobut...
Thanks
On Mon, 26 Sep 2011 14:24:36 -0500
"Rajesh Raju" <rajesh.raju.mail.chem.tamu.edu> wrote:
> Dear AMBER users,
>
> I have some common doubt about the MMGB/PBSA decomposition methods.
>
> [1] Wen I did the free energy decomposition for pairs resid 1 and
>resid 2 similar values but slightly different values. for example: 1
>and 2 the total value is -6.173 and for 2 and 1 the value is -6.154.
>The small difference comes from the term non-polar solvation. All
>other values are exactly the same.
>
> [2] The previous peril scrpit will divide the total decomposition
>between the pair. Is that the same procedue follow here in MMPBSA.py?
>For example if we do the QM calculation on the residues 1 and 2, the
>calculated interaction energy is ~13 kcal mol-1. So i assume that the
>binding free energy splitted between the two residues..So in order to
>comapre with the QM values we have to double it. If I am wrong pls
>correct me..
>
> [3] How the solvation free energy terms decompose. ? Since solvation
>free energy does not do anything with the other residues, Wat is the
>significance of this decomposition terms?
>
> [4] Is there any way to performe intra strand decomposition? I have
>performed decomposition between two modified DNA chains each
>containing 10 residues. When I did decompostion for all the 20
>residues, the decomposition energy values for the 1-2, 1-3, 1-4
>...1-9, 1-10 are 0.000 for all terms..I thought it would print the
>intrastrad binding free energy terms too..
>
> [5] The polar solvation decomposition value for the 2-2, 3-3, 4-4
>(dont know wat is the significance of the interaction of the residue
>with itself) prints some + values like +4 kcal mol-1..Wat does it
>mean?
>
> I hope these questions can help others too as I could nt find any
>details from manual....
>
> Thanks
> Rajesh
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Received on Mon Sep 26 2011 - 18:30:04 PDT
