[AMBER] ALASCAN (Alanine scanning mutagens )

From: Sushil Mishra <sushilbioinfo.gmail.com>
Date: Thu, 3 Jun 2010 19:09:36 +0200

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?

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Received on Thu Jun 03 2010 - 10:30:03 PDT
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