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

From: FyD <>
Date: Sat, 07 Jan 2017 19:33:39 +0100

Dear Azade,

> I have a problem similar to here <>.
> 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

The problem you underlined was reported mannnny times for antechamber,
and was corrected - not corrected?

If you use PyRED at RED Server Dev. 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

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Received on Sat Jan 07 2017 - 11:00:02 PST
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