[gmx-users] Force field parameterisation
Vitaly V. Chaban
vvchaban at gmail.com
Sun Aug 23 16:40:20 CEST 2015
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, Nash, Anthony <a.nash at ucl.ac.uk> wrote:
> 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
> tools) for partial charges and then parmchk2 for the bonded parameters. I
> would then need to do *something* to get it in an .itp format.
> I¹ve come a long way without need to use the Amber toolkit and I can¹t say
> I want to start now (although I have just downloaded it). Can this be done
> using anything Gromacs has to offer? Alternatively, does anyone know how
> go from an Amber .lib file to an .itp file?
> Many thanks
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