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

From: Azade Yazdan Yar <azade.yazdanyar.gmail.com>
Date: Thu, 5 Jan 2017 11:52:34 +0100

Hello everyone,

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?

Thanks a lot for your help.


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Received on Thu Jan 05 2017 - 03:00:02 PST
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