Dear Carlos and Rajeswari,
Thank you for your reply. Main point is folding difference between wt and a
mutant. Thank you again.
Batsaikhan
On Sun, Feb 28, 2016 at 1:32 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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 - 11:00:03 PST
