[gmx-users] Fatal error in atom

Dallas Warren dallas.warren at monash.edu
Sun Sep 22 23:57:11 CEST 2019

Did you look at the atom naming for the residue indicated? Does it have a
CA atom type within it? You need to open up the coordinate file you are
using as input, find residue 119, and ensure that all the atoms within that
residue are named corrected.

What the error is telling you is that residue 119, which is labelled as
GLY, should contain an atom with atomtype CA. However that CA atomtype is
not contained within the residue 119.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a

On Sat, 21 Sep 2019 at 17:06, Nandu TG <tg.nandu at gmail.com> wrote:

> Hi,
> I am beginner wit Gromacs, I am getting following error message during run.
> It would be highly appreciable if you helped me solve the problem.
> Fatal error:
> Residue 119 named GLY of a molecule in the input file was mapped
> to an entry in the topology database, but the atom CA used in
> that entry is not found in the input file. Perhaps your atom
> and/or residue naming needs to be fixed.
> Thanking you
> --
> Nandu T G
> Senior Research Fellow
> Division of Microbiology
> Jawaharlal Nehru Tropical Botanic Garden and Research Institute
> Palode, Karimancode
> Thiruvananthapuram-695562
> Kerala, India.
> --
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