Hi Justin,
indeed there are only six bonds in the topology files! As you said the
hydrogen nomenclature in .rtp file is wrong.
Thanks a lot!
Paolo
Il giorno gio 23 apr 2020 alle ore 12:55 Justin Lemkul ha
scritto:
>
>
> On 4/23/20 6:52 AM, Paolo Costa wrote:
> > Dear Gromacs Users,
> >
> >
On 4/23/20 6:52 AM, Paolo Costa wrote:
Dear Gromacs Users,
I am trying to perform MD simulations of benzene molecule in a cube of
water just for practicing.
By following the tutorial
https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/, I setup
the residue Benzene within Amber99
