Well there's your problem! Don't ignore things like this, the software is
giving you the warning for a reason.
You are going to have to go through that process again, and fix the
starting coordinate file you are using, or the processing, depending on
which atoms are the ones missing. The residue
I don't know where the non-integral charges come from. But When preparing the
gro file from the initial PDB file (a protein-DNA complex), I got a information
saying that there are 24 atoms missing in the structure, but I can't tell what
are these atoms. Could you tell me how to fix the atom
Go through the topologies, residue by residue, find where it deviates. Each
residue should sum to an integer charge.
Also look at how you generated the topology, actually steps involved, where
the coordinate files came from etc. Somewhere a choice has been made,
process performed that introduced
--
From:Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
Sent At:2019 Aug. 1 (Thu.) 12:31
To:gromacs ; 孙业平
Subject:Re: [gmx-users] How to deal with "non-zero total charge" problem in
gromacs?
Hi,
Yes you can use the (-maxwarn)
Hi,
Yes you can use the (-maxwarn) flag to overcome the error. But better
to optimize the starting structure to reduce the excess charge of your
system.
On Thu, Aug 1, 2019 at 9:35 AM sunyeping wrote:
> Dear all,
>
> I am trying to do MD simulation with protein-DNA complex with gromacs.
>
http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#system-has-non-zero-total-charge
You will need to go through your topologies and work out why there is a
non-zero charge like that.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash
Dear all,
I am trying to do MD simulation with protein-DNA complex with gromacs. When
using gmx grompp to generate the tpr file for energy minimization, I enconters
a fatal error:
Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.
There are
