[gmx-users] system has non zero net charge

[Gudrun Gygli]

Hi Yogesh,

this happens to me as well sometimes, there are several options:

- your protein is not neutral (my best practice is to you use pdb2gmx 
interactively and set the charges for all amino acids manually following 
pkA predictions by e.g. Propka - then you will immediately know if the 
protien has a charge from the output)

- one of your itp files (I guess POPC and U1NL are from ATB) has a 
non-zero charge - make sure to show 10 decimal points when you calculate 
the total charge of all the atoms in the ligands, it happens sometimes 
that these do NOT add up to a completely neutral value, and rounding 
errors will occur and mess up the total charge of your system - 
especially if you add 20 identical molecules.... It is always a good 
idea to carefully check the parameters obtained from ATB or another 
server - mistakes happen!

- if the charge persists, you must neutralise the system using genion: 
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-genion.html

Best of luck

Gudrun


Am 08.01.2020 um 12:01 schrieb 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.