On Mon, 6 Mar 2017 15:42:32 +0530
Smriti Sharma <ssmriti.gmail.com> wrote:
> Dear all,
>
> I want to compute relative del G binding of transformations of a
> protein-heme-CO system to protein-heme-O2 using TIMD. I am using
> different charge sets for both (heme-CO and heme-O2) though protein
> backbone charges are fixed. Please suggest, can i consider my lig1
> (=heme-CO) and lig2 (=heme-O2) with approximately 70-80 atoms?
You will have to include all atoms that differ in at least one force
field parameter. So it seems in your case the whole heme plus ligand
as you suggest.
> and Can study the 2 processes as
> Vo: heme-CO -> heme -O2
> V1: protein-heme-CO -> protein-heme-O2
This is the thermodynamic cycle but you have a V0 and a V1 for each
leg.
Cheers,
Hannes.
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Received on Mon Mar 06 2017 - 04:00:03 PST
