[gmx-users] system has non zero net charge

[Justin Lemkul]

On 1/8/20 6:01 AM, Yogesh Sharma wrote:
> 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.

Why is that unexpected? Your ligand is Si(OH)4 and likely participates 
in hydrogen-bonding interactions very easily with charged groups.

> 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.

The discrepancy between your value and -1 is simply due to rounding. The 
larger issue is you have a membrane system with a net charge. If you 
allow PME to apply a neutralizing background plasma to this system (i.e. 
you don't use counterions), you will get very severe artifacts.

> 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?

POPC is uncharged, water is uncharged, your ligand is uncharged, so the 
charge must be coming from...? :)

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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