> 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.
Does addions/addions2 take >1 ion? I vaguely remember doing this
for addIons at least (I wrote the code a while back).
> 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 should work.
> 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.
You can see what's in your molecule by 'desc protbox', and can
determine whether the unneeded addions is doing something wrong
by doing things step-by-step manually, or inserting 'charge protbox'
judiciously in your script. It sounds like there may be a bug
in there, be it leap or possibly your script.
Bill
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Received on Wed Aug 19 2009 - 22:18:30 PDT
