Please have a look at the following thread. It was suggested that you
cannot compare the G(wt) and G(mutant) directly. But you can compare the
delta G from both.
http://archive.ambermd.org/201511/0167.html
On 27-Feb-2016 6:44 pm, "Carlos Simmerling" <carlos.simmerling.gmail.com>
wrote:
> TI is usually considered to be more accurate, but takes more time to run.
> MMPBSA just requires the MD simulation for each mutant. You could start by
> looking at tutorials A3 and A9.
>
> On Sat, Feb 27, 2016 at 8:02 AM, Mahdieh Hadi <mahdieh.hadi.bric.ku.dk>
> wrote:
>
> > Thanks a lot. and which one is more accurate?
> >
> > ________________________________________
> > From: Carlos Simmerling [carlos.simmerling.gmail.com]
> > Sent: Saturday, February 27, 2016 1:48 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] How to analyze mutational free energy difference?
> >
> > this can be done either with TI or by using MD with MMPBSA, depending on
> > the level of accuracy that you need.
> >
> > On Sat, Feb 27, 2016 at 7:46 AM, Mahdieh Hadi <mahdieh.hadi.bric.ku.dk>
> > wrote:
> >
> > > I have almost the same problem. Which tutorial is suitable for ligand
> > > binding?
> > > ________________________________________
> > > From: Carlos Simmerling [carlos.simmerling.gmail.com]
> > > Sent: Saturday, February 27, 2016 1:39 PM
> > > To: AMBER Mailing List
> > > Subject: Re: [AMBER] How to analyze mutational free energy difference?
> > >
> > > what is the process for which you want the free energy? ligand binding?
> > > folding? activation? then we can suggest tutorials for that.
> > >
> > > On Sat, Feb 27, 2016 at 2:34 AM, Mijiddorj Batsaikhan <
> > > b.mijiddorj.gmail.com
> > > > wrote:
> > >
> > > > Dear users,
> > > >
> > > > I want to make mutational free energy difference of protein structure
> > > > (delta G = G wild-type - G mutant). If you do not mind, please give
> me
> > > > advice, and suggestions of related tutorials.
> > > >
> > > >
> > > > Batsaikhan
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Received on Sat Feb 27 2016 - 09:30:03 PST
