[gmx-users] Force field parameterisation

Nash, Anthony a.nash at ucl.ac.uk
Sat Aug 22 13:28:56 CEST 2015

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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