Thanks a lot for the response !
Yes I am getting fluctuation in binding energy by making the R17A mutation
but it is quite high change (about + 14 Kcal/mol). although I am trying to
repeat the calculation with much longer trajectory (15ns) and with more
number of snapshots (500 for each) so to avoid the problem of sampling. Can
u point out some issue which should be considered carefully during this type
of calculation ? could u direct me in any tutorial or paper regarding per
residue decomposition of free energy ?
Regards
Sushil
On Fri, Jun 4, 2010 at 4:52 PM, Dwight McGee <dwight.mcgee.gmail.com> wrote:
> Hi
>
> Based off the information below I would say yes to your approach. If you
> see a fluctuation in the binding energy from making the R17A mutation than
> you know whether or not that particular residue has an important
> contribution to the binding free energy. I am not aware of any tutorials,
> which demonstrate this using the mm_pbsa.pl though they might exist. There
> is however a tutorial demonstrating this using MMPBSA.py. No matter how
> many
> mutations you make at once it will only return back one free energy. You
> may
> want to look at doing Energy Decomposition because this will give you a
> better breakdown of each residue's contribution to the free energy.
> Good Luck
>
> On Thu, Jun 3, 2010 at 1:09 PM, Sushil Mishra <sushilbioinfo.gmail.com
> >wrote:
>
> > Hi all,
> >
> > I would like to share some experiences, with researchers tried Alanine
> > scanning mutagenesis using mm_pbsa.pl in amber 10. I am writing the
> steps
> > I
> > tried to attempt the problem (R17A mutation).
> >
> > 1 - I run a 20ns production run of protein with 12 A water box.
> > 2- run MM/PBSA calculation with wild type.
> > 3 - Then I mutated Arg17 in to Ala17 and created .prmtop and .inpcrd file
> > of
> > the mutated protein
> > 4 - I used that this prmtop file of complex and protein to run MM/PBSA
> > again. This time i used AS=1 and in .ALASCAN section i putted all the
> > information regarding mutation of Arg17 in to Ala17. As this info was
> > passed
> > to make_crd_hg and snapshot generated with these parameters were having
> > Ala17, so i used prmtop file fof rec and complex generated in step 3 for
> > calculation of free MM/PBSA.
> > 5- Now i compare the delta PBTOT of MM/PBSA run in wild type and delta
> > PBTOT
> > of MM/PBSA in mutant (R17A).
> >
> > Is the the correct way i used to find the change in free energy when Arg
> 17
> > was mutated in Ala17 ?
> > can u direct me to some tutorial where this thing have been tried with
> perl
> > script ?
> > As i read in manual it is possible to maximum 40 mutations in single run
> > but
> > will it return delta PBTOT of all 40 mutation at a time, or separately of
> > each one mutation at a time and for all 40 such mutatation?
> >
> > Regards
> > ..Sushil
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
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Received on Fri Jun 04 2010 - 08:30:03 PDT
