Re: [AMBER] ALASCAN (Alanine scanning mutagens )

From: Dwight McGee <>
Date: Fri, 4 Jun 2010 10:52:10 -0400


   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 though they might exist. There
is however a tutorial demonstrating this using 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 <>wrote:

> Hi all,
> I would like to share some experiences, with researchers tried Alanine
> scanning mutagenesis using 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
> 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

T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
"Problems cannot be solved at the same level of awareness that created
               Albert Einstein
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Received on Fri Jun 04 2010 - 08:00:03 PDT
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