[AMBER] relative binding free energy - tutorial a9

From: leila karami <karami.leila1.gmail.com>
Date: Sun, 4 Dec 2011 11:18:51 +0330

Dear Dr. Thomas Steinbrecher
I read amber - tutorial a9 (from atila petrosian) in amber mailing list.

I want to do relative binding free energy analysis for my system
(protein-dna comlex).

In my case, ligand is dna. I will investigate mutation of the dna (for
example, T ---> G). My thermodynamic cycle is as follows:

mdna = mutated dna

                                    delta G1

            Protein-dna ----- protein-mdna

delta G3 | | delta G4

                dna ----- mdna

                                    delta G2

I want to calculate delta delta G = delta G2 - delta G1 = delta G4 - delta
You broken up each transformation into three substeps : 1) Remove charges
from BNZ 2) Transform BNZ into PHN and 3) Add charges to PHN.

I want to know should I use 3 substeps also?

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Received on Sun Dec 04 2011 - 00:00:03 PST
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