[gmx-users] Net charge error

Justin Lemkul jalemkul at vt.edu
Sun Jan 11 16:26:53 CET 2015

On 1/11/15 10:23 AM, Siddhesh Kamat wrote:
> Hello everyone,
>   I am working on a monoprotic Napthenic acid(a simple straight chain one
> C29H59COOH). I made the .itp file and used PRODRG for the .gro file. I am
> unable to energy minimise the system after adding TIP4P water. The error I
> am getting is 'net charge is non zero and the number it gives is about
> 453(it gives a decimal actually). I have thoroughly checked the .itp and

Please copy and paste the exact error message from the terminal.

> .top files. The number that GROMACS gives is actually very close to the
> total mass of the system. I am using GROMACS version 5.04 and I am

So did you perhaps invert the mass and charge columns in the topology?

> relatively pretty new to GROMACS. Please suggest what may be the possible
> problem.

If you can provide a link to download your topology, that would help.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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