[gmx-users] Re: Too close water molecules

saurabh shakya shakya_79 at yahoo.com
Tue Jan 6 15:52:01 CET 2004

Would it be possible to specify the dihedrals
involving the Fe as improper rather than RB ? would it
be same ?

On Tue, 2004-01-06 at 15:36, saurabh shakya wrote:
> Making the addition to specbond.dat as you suggested
> helped to get rid of the extra Hg ,but on running
> grompp for em i get the following error message 
> > No default Angle types, using zeroes
> No default Ryckaert-Bell. types, using zeroes
> > These messages are for the angles and dihedrals
> involving Fe . Angle default values and force
> constants can be given manually but how do I set the
> RB parameters.
Not trivial. If you don't have something very similar
you'll have to
parameterize the torsion, check the Jorgensen papers
on the OPLS force
field. On the other hand, there is probably not much
happening in that
region of your molecule, so you could add a RB
potential that has the
correct minimum angle. Alternatively you could even
leave it out.

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