The only thing you need is to transfer partial charges. This can be
done using a copy-paste tool.
The Amber FF is within gromacs distribution, so the needed bond
lengths will be picked up implicitly after you specify bonded atoms,
e.g. using x2top or by hand.
On Sat, Aug 22, 2015 at 8:28 AM,
Hi all,
I am trying to parameterise a new compound in Gromacs (theoretical
compound - my experimental collaborators are still trying to purify and
mass spec it) using the Amber 99sb force field. After asking about, I now
know that in Amber I would take my QM structure run antechamber (or R.E.D
