AMBER Archive (2009)

Subject: [AMBER] sourcing leap commands in log file

From: Donald Keidel (dkeidel_at_scripps.edu)
Date: Wed Aug 12 2009 - 19:32:31 CDT

I have automated some leap runs. In these I neutralize the charge of a
solvent box around my protein using the addIons2 command. Sometimes,
depending on the system, the charge before I add ions is negative other
times it is positive. Since I do not know a way for the leap script to
be smart and choose the proper command based on the charge of the system
after solvent added. The 2 commands that I have in the leap script to
cover both possibilities described above are:

addIons2 protbox Na+ 0
addIons2 protbox Cl- 0

This way if the charge is negative the 1st command to be the one needed,
it the system is positive the second will be needed. My question is the
following:

For a system I am looking at the charge was negative after solvent added
so the first command in the leap script was the one that was needed.
But the second one was also be executed since it is in the script for
systems that have positive charge. I am wondering if executing the
second command will cause leap to remove the Na that was already added.
The reason I ask this is because here is the output from leap:
.
.
.
.
Calculating grid charges
charges: 2522 sec
Placed Na+ in protbox at (-25.08, -1.12, 3.72).
Placed Na+ in protbox at (-9.08, -6.12, -12.28).
Placed Na+ in protbox at (20.92, 14.88, 0.72).
Placed Na+ in protbox at (-12.08, 1.88, -8.28).
Placed Na+ in protbox at (42.92, 24.88, -28.28).
Placed Na+ in protbox at (-1.08, 7.88, -35.28).
Placed Na+ in protbox at (42.92, 33.88, 15.72).
Placed Na+ in protbox at (16.92, -15.12, -35.28).
Placed Na+ in protbox at (42.92, 5.88, 27.72).
Placed Na+ in protbox at (42.92, 5.88, 8.72).
Placed Na+ in protbox at (40.92, 35.88, -2.28).
Placed Na+ in protbox at (-42.08, 4.88, 30.72).
Placed Na+ in protbox at (-6.08, -36.12, 2.72).

Done adding ions.
  0.000000 0 1 0
(I execute the command: addIons2 protbox Cl- 0 here in the script)
0 Cl- ion required to neutralize.
Adding 0 counter ions to "protbox" using 1A grid
Checking Unit.
WARNING: The unperturbed charge of the unit: -13.000000 is not zero.

  -- ignoring the warning.

Na has been added, but the part that concerns me is the WARNING: The
unperturbed charge of the unit: -13.000000 is not zero. This leads me
to believe that the Na+ added is no longer there since that overall
charge is not zero.

Please let me know if this is the case.

Thank you very much.

Don 

-- 

_______________________________________________________________________

Donald J. Keidel, Ph.D.
Research Associate
The Scripps Research Institute
3377 N. Torrey Pines Court, Suite 100
La Jolla, CA 92037
mail code: TPC-26
phone:  (858) 784-2842
fax:  (858) 784-2341
dkeidel_at_scripps.edu
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm

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