AMBER Archive (2008)

Subject: AMBER: mm/pbsa and saltcon effect

From: Christopher Gaughan (clgaughan68_at_gmail.com)
Date: Fri Jan 04 2008 - 15:40:17 CST

Hello,

I have been trying to see the effect of increasing the salt concentration on
the delta G of binding of a dimer consisting of two 28aa alpha helices using
mm-pbsa algorithm. I have noticed no effect of changing this parameter even
up to 5M concentration of counterions. I have attached the
statistics.outfiles of an mmpbsa run with 0 salt and a
statistics.out file for a run where saltcon is set to 5M. This strikes me as
very unusual since the dimer is supposedly partially held together by
electrostatic forces (Lys-Glu interactions). Surely 5M salt should have had
some effect.

Here is my setup:

MM 1
GB 1
PB 1
MS 1

IGB 2
GBSA 1
SALTCON 5.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00

Can anyone see anything wrong here?



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