Re: [AMBER] antechamber: why the net charge does not sum up to zero?

From: Jason Swails <>
Date: Thu, 5 Jan 2017 12:55:23 -0500

On Thu, Jan 5, 2017 at 5:52 AM, Azade Yazdan Yar <>

> Hello everyone,
> I have a problem similar to here <
> 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?

​The only comment I'll make in addition to what Hannes said is that unless
you plan on using the generated mol2 file as a template for a solvent
molecule -- that is, unless you plan on including many thousands of copies
of this residue in your system -- the round-off error of 0.01 to 0.001 will
make little to no difference (values this small get smeared over every atom
in the system by sander and pmemd).

If you plan on including many thousands of copies, then the net charge may
start to become significant (although the net neutralizing plasma will
still be able to handle this excess charge for most applications).
However, ParmEd has the ability to redistribute this excess charge to yield
a set of charges that round to an exact integer for any level of precision
you want in the charges.

This can be accomplished with a quick Python script that looks like this:

import parmed as pmd


This needs to be invoked with the amber.python interpreter to make sure
that ParmEd can be found. However, as mentioned before, unless you plan on
including thousands of copies of this residue in your system, there is
nothing to worry about.


Jason M. Swails
AMBER mailing list
Received on Thu Jan 05 2017 - 10:00:04 PST
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