[gmx-users] Atomtype HC not found

Mark Abraham mark.j.abraham at gmail.com
Tue Apr 24 15:51:32 CEST 2018


As it says, your topology wants to use atom type HC, and it isn't found. So
you need to somehow use forcefield files that describe HC. That probably
means double checking that you did the tutorial steps properly.


On Tue, Apr 24, 2018 at 2:40 PM Giordano Perini <giordano.perini13 at gmail.com>

> Dear all,
> I've built a Graphene in water topology in order to simulate it. I've
> obtained Graphene structure from VMD (Nanotube builder) and I was able to
> generate the topology by following the instructions of the tutorial of
> Andrea Minoia.
> While running the following command:
> gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
> I recieve as error:
> Source code file:
> /home/giordano/Downloads/gromacs5.1.1/src/gromacs/gmxpreprocess/toppush.c,
> line: 1353
> Fatal error:
> Atomtype HC not found
> Since I am new in Molecular Dynamics simulations, I am asking you to help
> me understand where I got it wrong and what can I do to solve this problem.
> Giordano Perini,
> PhD student, Institute of Physics, Catholic University of Sacred Heart,
> Italy, Rome.
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