[AMBER] saltconc and string parameters in MM/PB(GB)SA

From: mish <smncbr.gmail.com>
Date: Thu, 8 Mar 2012 18:34:00 +0100

Dear all:

I have question related to salt the salt concentration and ionic strength
values used in MM/GBSA and MM/PBSA calculations, respectively. Initially I
was using perl script and I did not care much about these two values ( so
they were set to zero). Now when I switched to new python script, I noticed
in the manual that value of saltconc was set to 0.15 (for IGB=5) and 0.10
(for igb=2) in sample input file. Also istrng=0.15 is mentioned for PB

I want to know, if this should effect the binding energies too much ? and
also the reason to have those values (when default is 0.0) there in sample
input files of manual ? I looked for experimental detail in my case and
what I can see is ITC measurement were done in 100mM Tris buffer at pH 7.5
. Can you please suggest me optimal (theoretically) values of saltconc and
istring to compare these experimental values taken in 100mM Tris buffer at
pH 7.5 ?

Thanking you.
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Received on Thu Mar 08 2012 - 10:00:03 PST
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