[gmx-users] problem in grompp -broken charge

[Mark Abraham]

Samik Bhattacharya wrote:
> hi,
> Justin, i have completed upto the genion step of that simulation. One 
> error is creeping in this step which is nonzero system charge. my system 
> is said to have a charge 1.69. now how to neutralize this kind of broken 
> charge? another thing is that how this kind of broken chage is being 
> developed? i think something was wrong in previous steps. but can't 
> recognise which step to account for this anomalous behavior? waiting for 
> your valuable suggestions...

Probably you have broken termini. Go and read all of the output from 
pdb2gmx carefully. If that doesn't clue you in, look at the [atoms] 
section of your .top file. There's a running count of the total 
charge... whenever that first becomes non-integral for the last atom in 
a residue, you have a broken residue there.

Mark