[AMBER] A bug with unperturbed charge during tleap processing

From: James Starlight <jmsstarlight.gmail.com>
Date: Wed, 2 Aug 2017 20:16:02 +0200

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?



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Received on Wed Aug 02 2017 - 11:30:02 PDT
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