See i think if you need the automated shell script, do one thing.
For all the considered systems, make a file with pathnames appended.
Run a for loop for the file.
put a charge command in the loop.
If it is positive addions2 protbox Na+ 0
If it is negative addions2 protbox Cl- 0
now check the charge again at the end with all your required
parameters in between in this shell script.
Now verify the charge again at the end.
If it is zero kill the script.
I guess thatz all what you need.
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.
On 8/13/09, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> 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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>
--
Ashish Runthala,
Faculty Division III,
Assistant Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA
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Received on Wed Aug 19 2009 - 22:36:01 PDT
