[gmx-users] system has non zero net charge

[Yogesh Sharma]

Greetings,
I am performing membrane protein simulation in the presence of a
biomolecule. topology for the molecule was downloaded from ATB server.
After simulation run, I found unexpected behviour of the added
biomolecule.  This ligand named UINL was showing affinity to ASP and GLU
residues. ligand didnt seperate through out simulation once bound, which is
highly unexpected at neutral pH.

I was getting these two notes during solvation.

Generated 1062 of the 3486 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'POPC'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'U1NL'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...

NOTE 1 [file topol2.top, line 18875]:
  System has non-zero total charge: -1.000002
  Total charge should normally be an integer.

Is it possible this -1 charge is producing artifact. I have addded 20
molecules of same ligand in my system and 6 of them are binding to negative
charged residues.
I checked total charge on ligand.itp file, its zero. then i checked line
18875 in topol2.top its SOL which is highly unlikely to have any charge.

U1NL     3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass
    1  HS14    1    U1NL     H4     1    0.480   1.0080
    2 OEOpt    1    U1NL     O4    2   -0.814  15.9994
    3    SI         1    U1NL     Si     3    1.336   28.0800
    4 OEOpt    1    U1NL     O1    4   -0.814  15.9994
    5  HS14     1    U1NL     H1     5    0.480   1.0080
    6 OEOpt    1    U1NL     O2    6   -0.814  15.9994
    7  HS14     1    U1NL     H3     7    0.480   1.0080
    8 OEOpt    1    U1NL     O3    8   -0.814  15.9994
    9  HS14    1    U1NL     H2     9    0.480   1.0080
; total charge of the molecule:  -0.000

How can i check what molecule is throwing this negative -1 charge to my
system?
Thankyou in advance for your valuable time.