I agree, and in fact I don't think its straightforward to calculate G
itself anyway, deltaG is much easier. but again, it really depends on the
process for which you want to compare wild type and mutant. there are many
methods for free energy calculation, and it's hard to recommend one without
knowing what the actual endpoints are.
On Sat, Feb 27, 2016 at 12:11 PM, Rajeswari A. <rajeswari.biotech.gmail.com>
wrote:
> 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 - 10:00:03 PST
