AMBER Archive (2009)

Subject: [AMBER] Proper ISTRNG value ?

From: Marek Maly (marek.maly_at_ujep.cz)
Date: Fri Jun 05 2009 - 11:24:58 CDT

Dear Amber users,

I would like to do mm_pbsa analysis of my charged system which was
simulated in explicit water and
with contraions. The ionic strength 150mM. I am using Amber10.

In mm_pbsa input file is parameter ISTRNG.

I think that the value of this parameter should be 150 in my case but I am
not sure
since everywhere I saw some examples, there is usually ISTRNG=0, although
everybody
probably uses contraions when simulate charged molecules in explicit water.
So it is really OK to set this parameter 150 in my case ?

I have also made some test to find out the influence of this parameter on
calculated value of dH regarding to my system (1 receptor + 1 ligand).
Here are the results:

ISTRNG dH
0 -116.79 -116.79 -116.79
150 -116.91 -116.97 -117.00
1500 -117.40 -117.68 -117.9

It seems that the influence of this parameter is really minor. I also
found out
that if I run the calculation with the same ISTRNG value several time, I
obtain slightly different
values of dH except the setting ISTRNG=0. It seems that using different
value from 0 involves
some stochastic part to the calculation, am I right ?
The last thing which is a little surprising for me is that with increasing
of ionic strength there
is better binding between the receptor and ligand, which is in the case of
electrostatically atracted
molecules a little surprise for me since higher ion concentration = higher
screening of the receptor and ligand
charge. But I am not an expert here ...

Thanks in advance for any comment !

    Best,

       Marek 

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