---------- Forwarded message ----------
From: BERGY <nucleic81.gmail.com>
Date: Tue, Feb 5, 2013 at 8:31 PM
Subject:
To: AMBER Mailing List <amber.ambermd.org>, Rashmi Panigrahi <
rashmi.panigrahi19.gmail.com>
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
