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 Wed Aug 02 2017 - 22:00:03 PDT
