Thanks for your reply Hannes.
You pointed out correctly, charges are different for (heme-lig units) and 1
atom amongst the ligands is different.
I mentioned incorrectly, V0 and V1 will be for the transition from state1
to state2 in with or without complex in solution. those equations were
meant for del G computation, a thermodynamic cycle.
Thanks & regards
Smriti Sharma
On Mon, Mar 6, 2017 at 5:13 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
wrote:
> 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 - 20:00:02 PST
