Re: [AMBER] A bug with unperturbed charge during tleap processing

From: James Starlight <>
Date: Thu, 3 Aug 2017 10:27:19 +0200


Regarding the ions - the system consists of only Cl-, so the charge
might became +1 positive if I removed one ion ocasionally.

But for the test I modify my workflow - to ad CL- ions on the second
step (in the pdb where water have already been cut).
So now there is no warnings but as expected it adds one negative ion
less (13 added) compared to if I would add Cl ions on the first step
(14 added) :-)
Thus after the second processing of tleap the total charge has been
changed to +1 althought I didn'd change nothing.
I have checked the termi group of the protein - it looks like H1 H2 H3
N of one side and C O Oxt on the other side. Also there were no any
modifications with a protein loaded in both times (before and after
cut of water)

P.S. this strange I found in the first tleap log when it also added a hydrogens
total atoms in file: 10039
  Leap added 8132 missing atoms according to residue templates:
       8132 H / lone pairs
  The file contained 1 atoms not in residue templates

How I can test in tleap the source of the charge e.g to print all
charged entities in loaded pdb?


2017-08-03 6:31 GMT+02:00 Bill Ross <>:
> Are you sure you didn't remove an ion when removing waters manually?
> And you verified that the 1st log file didn't contain the warning?
> Bill
> On 8/2/17 11:16 AM, James Starlight wrote:
>> Dear Amber users!
>> I found a small bug during processing of my system via tleap.
>> Briefly I have to apply tleap 2 times for my system:
>> 1- to solvate the assembled system with TIP3P and ions
>> 1b - manually cut some unused water from the pdb which I have obtained from 1).
>> 2- apply tleap agai, to make final params and coordfinates for my
>> system with reduced number of water.
>> There is nothing strange with both steps but in the second log of
>> tleap I found a warning:
>> Checking Unit.
>> WARNING: The unperturbed charge of the unit: -0.999703 is not zero.
>> -- ignoring the warning.
>> To fix it I add POT ion during second step of tleap processing
>> addIons: 1st Ion & target are the same charge:
>> can't neutralize.
>> 1 K ion required to neutralize.
>> Adding 1 counter ions to "protein" using 1A grid
>> Grid extends from solute vdw + 1.71 to 8.22
>> Resolution: 1.00 Angstrom.
>> grid build: 1 sec
>> Solvent present: replacing closest with ion
>> when steric overlaps occur
>> Calculating grid charges
>> charges: 61 sec
>> (No solvent overlap)
>> Placed K in protein at (21.44, 13.83, -20.24).
>> So the question - why the charge has been altered after a second
>> application of tleap, assuming that I only changed number of water in
>> pdb resulted from first call of tleap?
>> Could it be due to the changing of the protonation states of the N or
>> C term of the protein (when I apply the tleap second tiime) and how it
>> can be fixed?
>> Thanks!
>> James
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Received on Thu Aug 03 2017 - 01:30:02 PDT
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