Date: Mon, 24 Oct 2016 14:03:57 -0400
Dear all,
I ran a simulation for protein complexes which includes four chains as
shown below. Protein "C" is a dimer and protein A binds to protein C and I
am interested to run MM-PBSA to estimate binding free energy between
protein A and protein C in its dimeric form.
Fo MM-PBSA, I created a separate PDB file for A and another PDB file with
the rest of the proteins (C-C dimer +another A). Then for the MMPBSA
command I treated A as the ligand protein and C-C dimer + A as receptor
protein. I ran with the following script:
&general
|startframe=4501, endframe=5550, interval=5,
|verbose=2, keep_files=2, strip_mask=':WAT,CL',
|/
|&gb
|igb=8, saltcon=0.150,
|/
|&pb
|inp=1, radiopt=0, istrng=0.15, fillratio=4.0
|/
When the run was done I checked the Delta delta G and it came to be about
1000 kcal/mol which I think is way too high for the interface.
Previously, I have separately ran and analyzed the Delta delta G without
the dimer where there is only one A and one C the Delta delta G was -60
kcal/mol.
So I am sure I am not either setting these different PDBs right or may be I
am missing something important while setting up for MM-PB/GBSA analysis.
How do I approach this problem?
Any insight would be really appreciated.
[image: Inline image 2]
Sincerely,
Jag
Graduate Student,
Michigan State University
Department of Chemistry
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