[AMBER] Decomposition Energy Problem with Aspartic Acid only

From: Jag Silwal <jagsilwal.gmail.com>
Date: Fri, 11 Aug 2017 12:18:45 -0400

Dear All,

I am having some issues with Aspartic acid residues when I plot the
decomposition energy.

After 180ns of simulation run, I did alanine scanning and decomposition
energy analysis. Everything else looked OK except for aspartric acid
residues. The decomposition energy for Aspartic acid for all the proteins I
have been working with is positive. Weird thing is that when I did alanine
scanning mutagenesis in Amber, the delata-delta G is way negative for the
same aspartic acid residue.

 Also this aspartic residue makes hydrogen bond interaction with an
arginine residue at the protein interface. Alanine scanning and
decomposition energy data for this arginine are fine. But it didn't make
sense to me that its pair for hydrogen bonding,aspartic acid in other
protein, has much larger positive decomposition energy.
 I am using mbondii3 and igb 8. Could someone please help me figure this
out? My other colleague also got this weird high positive value for
aspartic acid only for his protein.

Any help would be greatly appreciated.


Jag S

Michigan State University
Department of Chemistry
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Received on Fri Aug 11 2017 - 09:30:02 PDT
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