Hi all
just to add to it
In my proteini have
NATIVE:DELTA TOTAL * -13.7358 * 6.7266
0.6727
V123A MUTANT:
POISSON BOLTZMANN
MUTANT:DELTA TOTAL * -7.5677 * 6.7846
0.6785
RESULT OF ALANINE SCANNING: (V123A) DELTA DELTA G binding = * -6.168*1
+/- 1.0955
This tell me that Native minus mutant is carried out and negative value
indicates that alanine mutation destabilize the interactions.
Hope I am correct here.
On Tue, Feb 5, 2013 at 8:31 PM, BERGY <nucleic81.gmail.com> wrote:
> Hi all i carried out MMPBSA alanine scan using amber12 MMPBSA.py.
> I found that the criticall residues mutated gave me a Negative value
> instead of positive value.
> Then i went and rea some papers and many said Dela-Delat G =
> DelatG(Mutant) minus DeltaG Native.
> and the value will be positive.
>
> SO i did the tutorial on alanine scanning
> it just addded more to my confusion
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section3.htm
>
> i am pasting the values given in tutorial page first (only PB given)
> NATIVE: DELTA G binding = -89.9575 +/-
> 8.2480 1.1664
> MUTANT: DELTA G binding = -87.8385 +/-
> 8.0665 1.1408
>
> and the so the
> RESULT OF ALANINE SCANNING: (I21A MUTANT:) DELTA DELTA G binding =
> 2.1190 +/- 11.5368
>
> Its coming positve which means: Mutant(-87.8) minus Native(-89.9) =
> 2.1190)
>
> Here comes the problem.
> Whne i repaetd the tutorial
> i got the opposite
> My result for RAS_RAF is
> NATIVE: DELTA TOTAL -28.3249
> 8.3093 1.1751
> MUTANT:DELTA TOTAL -25.8148
> 8.3300 1.1780
>
> RESULT OF ALANINE SCANNING: (I21A) DELTA DELTA G binding = -2.5100
> +/- 0.8185
>
> Here the results say that
> Its coming negative which means ( native(-28.3) minus Mutant(-25.8)=
> -2.5).
>
> I feel somewhere down the line the A-B has got interchanged to B-A...
> Can some one explain which is correct. Please not that i understand that
> i used amber12 and the tutorial might have been done in old mmpbsa. but
> even then its the difference in value that matters. I think the
>
> This paper
> http://depts.washington.edu/bakerpg/papers/FriApr3012:42:182004.pdf
> says Positive values mean that replacement by alanine is predicted to
> destabilize the complex;
> ans it uses native minus mutant.
>
>
> In this paper,
> http://peds.oxfordjournals.org/content/24/1-2/197.full
>
> they say Mutant minus native ????
>
> which is correct. i guess in the end i shwed just see the delta G values
> individually for native n mutant
>
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Received on Tue Feb 05 2013 - 07:30:03 PST
