One immature way is to add -0.001 e to any atom of .mol2 file and then the
net charge is zero, if you are disgusted at this non-integral net charge. I
believe the physical/chemical/biological picture would not be changed with
-0.001 net charge;
jing
On Sat, Jan 7, 2017 at 8:33 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Azade,
>
> > I have a problem similar to here <http://archive.ambermd.org/
> all/2855.html>.
> > Unfortunately, I did not find an answer to that inquiry.
> >
> > I am using antechamber on a pdb file to create the mol2 file.
> >
> > The molecule should be charge neutral and I am using ‘-c bcc –nc 0’
> flags.
> > However, the sum of the charges in the output.mol2 generated by
> antechamber
> > is not 0.0.
> >
> > I also tried ‘-ek maxcyc=0’ flag on several initial.pdb files (point 7,
> > P.277 of the manual) which all of them lead to a non-zero net charge. The
> > smallest net charge which I can get is 0.001.
> >
> > My question is whether or not this net charge is small enough so I can
> work
> > with it or is there is another trick which I can use?
>
> If one uses/selects a charge accuracy at 1.10-4 one should get 0.0000
> as a total charge for a neutral molecule (this is quite basic).
> If one uses a charge accuracy at 1.10-3 one should get 0.000 as a
> total charge for a neutral molecule.
>
> The problem is not to get 0.001 for a charge accuracy of 0.000 (this
> error is acceptable); the problem is to get 0.0010 for a charge
> accuracy of 0.0000: here there is something wrong (because of charge
> equivalencing?)
>
> The problem you underlined was reported mannnny times for antechamber,
> and was corrected - not corrected?
>
> If you use PyRED at RED Server Dev.
> http://q4md-forcefieldtools.org/REDServer-Development/ this problem is
> fully handled for whole molecules _and_ molecular fragments whatever
> is the selected charge accuracy (1.10-4 is the default).
>
> regards, Francois
>
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
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Received on Sat Jan 07 2017 - 12:30:03 PST
