[gmx-users] how to do neutralization?

[João Henriques]

​That can't be right, AMBER03 does not contain amino acid residues with
partial charges. Each residue's charge is parametrized for a final integer
net charge. Are you using any custom/modified residue blocks? If not, when
you pass the PDB of a protein to pdb2gmx, and that protein containing aa.
residues that are defined in the force field​ rtp file, pdb2gmx will
produce a topology with integer net charge. It is generally a good idea to
tell pdb2gmx to ignore the hydrogen atoms present in the PDB file and set
the protonation states on the fly (using the -ignh and -inter flags).

Now, if you're tampering with the rtp and itp files and/or parametrizing it
yourself, that's a completely different story. AMBER03 and GROMACS are not
to blame, it must be whatever the user is doing. From experience, I can
tell you that a properly performed parametrization will yield no such
issues. But it's difficult to evaluate the problem you're trying to
describe without further detail.

J


On Thu, Nov 2, 2017 at 11:31 AM, rose rahmani <rose.rhmn93 at gmail.com> wrote:

> HI,
> I have the same problem,i use AMBER03 force field,the structure has Zn and
> S atoms and amino acids with net charge less than 1, idont know what should
> i do,i optimized the structure in Gaussian and put H atom for make it more
> stable but its not included in itp file.
>
> On Thu, Nov 2, 2017 at 1:23 PM, João Henriques <
> joao.m.a.henriques at gmail.com
> > wrote:
>
> > Hi,
> >
> > What system is that and what force field are you using? Building blocks
> > usually have integer net charges, this is rather unusual.
> >
> > Cheers,
> > J
> >
> > On Thu, Nov 2, 2017 at 10:02 AM, Seera Suryanarayana <
> palusoori at gmail.com>
> > wrote:
> >
> > > Dear gromacs users
> > >
> > > I got the system non-zero total charge: -0.226000. When I add one NA
> ion
> > to
> > > the system I got non-zero total charge: +0.77. What is the way to
> > > neutralize the system?
> > >
> > > Thanks in advance
> > > Surya
> > > Graduate student
> > > India.
> > > --
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