Re: [AMBER] Two questions about Net charge and write frcmod in

From: Jason Swails <>
Date: Thu, 18 Sep 2014 07:29:31 -0400

On Wed, 2014-09-17 at 21:36 -0400, Arun Srikanth wrote:
> Hello. I have two questions,
> First question:
> I have calculated the partial charges using am1bcc for the atoms in my
> molecule (from antechamber). I generated the topology file from the mol2
> file from leap. But when I check the netcharge using It is not
> zero.
> It is showing a value of -0.001 for the molecule. Can this be neglected
> during a simulation. I am simulating a bulk system so this charge (-0.001)
> scaled by the system size is giving a warning in my simulation.

Yes, you can ignore this. If you wanted to, you could add a charge of
0.001 to one of the atoms in your mol2 file to force it to be neutral
(or you can spread that 0.001 out across several atoms -- it's so little
charge that it won't make a noticeable difference).

> Second question:
> When I use the write Frcmod to see the parameters defined in the topology
> file. It shows that the bond coefficients are defined multiple times. For
> eg
> ca - c3
> c3 - ca
> both have the same coefficients.
> I need unique bond types from write Frcmod. I can write script to get the
> unique bond types but is there any other way ?

I wasn't aware that it printed duplicates. What version of AmberTools
are you using? Can you send me the example topology file so I can check


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Sep 18 2014 - 04:30:06 PDT
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