[gmx-users] Format of a Topology File When Using Amber FF in Gromacs

[Mark Abraham]

> [Question 1] The topology file produced by pdb2gmx with Amber FF
> (ffamber03, for example) looked different from what we used to obtain with
> ffG43a1.
>
> No force constants were assigned in [ bonds ], [ angles ], [ dihedrals ],
> etc.

That's because they're being read from ffamber03bon.itp by grompp when the
time comes, according to the atom names/types.

> [Question 2] In the RTP file of Amber FF, again no force constants were
> assigned in [ bonds ], [ dihedrals ], etc., and [ angles ] was missing.
>
> Is it what it¡¯s supposed to be?

pdb2gmx generates angles, pairs, exclusions, etc. based on the bonding
connectivity and the defaults for the force field.

Mark