Subject: Summary: InsightII, PBC, Counter ions, Protein

From: "Jianhui Wu" <[email-masked]>
Date: Wed, 08 Dec 1999 10:17:24 -0500

Dear all,

Last week I asked a question regarding how to add counter ions in a PBC
discovery calculation. I would like to thank Dr. Marek Orzechowski and
Dr. Eberhard von Kitzing for their advice. This is the only two advice I
got
up to now. If you have more advice, please direct it to me. I will
summarize
them again if I get more response.

Regards,

Jian Hui Wu
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Original question:
> Dear all,
>
> I am trying to model ligand-protein interaction using discovery within

> InsightII (version 97). I would like to solvate the system by PBC
water
> box. The protein has –12 charge (ligand is neutral). Is it essential
to add
> the counter ions in the system to neutralize the net charge before
>a PBC discovery calculation (MM or MD) is performed?  (Probably, yes)
>
> I find counter_ion.bcl in the $BIOSYM/gifts/insight/BCL/ directory.
> It is for DNA stuff. It seems that 12 Na+ ions have to be put into the

> 12 most negative charged position (somewhere in the protein, I guess),

> how can I find these position?
>
> Any help will be greatly appreciated.
>
*************************************************************
Advice:
(1)  Eberhard von Kitzing <[email-masked]>

The Maxwell relaxation time (see introductions into semi conductor
physics) is the time needed by the system to equilibrate. It is
in the order of lDH^2/D where lDH is the Debye length and D the
diffusion constant of the ions. Thus, to add salt in addition to
the excess charge would improve the equilibration of your simulation.
Test calculations done by others showed that such additional salt
generally stabilizes the simulation.
**************************************************************
(2)  Marek Orzechowski <[email-masked]>

...As far as I understood your problem is connected with positions of
counterions
in a cell.I am just curious whether You had no problems with assigning
charges
because this was my problem.I didn't use counter_ion.bcl file, but took
one atom
of Na ,put charge +1 on it and tried to assign charge,potential and
partial charge
using forcfield pulldown.And it didn't work.
But returning to your problem I think that You don't have to bother
about positionning
Na+ ions ,because during minimization they find the best positions.This
is my
personal opinion ,but seems to be resonable.What do You think?Attraction
between Na+
and charged groups in protein is strong enough to place Na+ in right
positions.
You have to ,of course fix the protein first.
Remember of the value of cutoff You use for electrostatic interactions.
I can advise You not to use the file *.bcl ,but did somthig what I have
done.
Take one atom of Na, using forcfield pulldown assign everything, what is
needed
(probably You'll see: Warning!Total formal charge is not equal partial
charge or something
simmilar - it depends on the forcefield You use), then take 12 atoms of
Na
(as You need) and do the same putting them first  in the cell wherever
You want.
Assign charges and potential types and edit files *.mdf
and *.car writting 1+ instead of 0 (in the positions of charges of
Na+),how it
is after doing as described above (if You had the warning ,of course ,if
not Your're
lucky and You don't have to edit anything).
Best wishes ,
Marek
*************************************************************
E.O.F