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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> > >
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Received on Sat Feb 27 2016 - 05:30:06 PST
