[gmx-users] build up ffgmx2 forcefield topology file

Erik Lindahl lindahl at stanford.edu
Tue Oct 15 19:31:49 CEST 2002

刘 松柏 wrote:

> hi, everyone:
> I'm wondering what I did. When I run 'grompp' to minimize energy of a
> small molecule, there're many warnings"No default Angle types, using
> zeroes", so I decided to add the parameter myself. I got the ffgmx2
> topology using pdb2gmx with option "-dummy hydrogens", and I think
> since the hydrogens are dummy I can copy corresponding parameters from
> ffgmx topology file which was built from PRODRG and delete items
> including hydrogens. Does it make sense?

The ffgmx2 force field isn't a real all-atom force field, it just has
hydrogens without interactions to facilitate NMR restraints.

If you really want an all atom force field it's much better to use OPLS.



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