[gmx-users] dummy atoms

[Frank Wennmohs]

On Tue, Oct 22, 2002 at 10:16:00PM +0200, David van der Spoel wrote:
> On Wed, 2002-10-23 at 11:19, Frank Wennmohs wrote:
> > On Tue, Oct 22, 2002 at 10:05:49PM +0200, David van der Spoel wrote:
> > > On Wed, 2002-10-23 at 11:08, Frank Wennmohs wrote:
> > > > Hello all!
> > > > 
> > > > Is it possible that there are some restrictions
> > > > as to where dummy atoms can be placed in
> > > > a molecule's topology?
> > > > 
> > > > As I performed the following scenario:
> > > > I inserted dummy atoms in a protein topology generated
> > > > by pdb2gmx and renumbered all atoms and charge groups thereafter.
> > > > Afterwards gmx complained about not defined angles like
> > > > simple backbone angles!
> > > > 
> > > > 
> > > > Has anyone an explanation for this?
> > > DId you also renumber all the angles and bonds etc.?
> > > > 
> > > > 
> > Yes, I did a complete renumbering.
> > I also checked the entries in angles, bonds etc. as to
> > which atoms they are referring to.
> > 
> > Everything seems correct in the top.
> > But he is complaining only from the point of change
> > onwards. 
> Nevertheless this kind of error message is usually accurate. Normally
> the angles etc. are defined based on the atomtype. If you changed that
> (to e.g. dummy) it won't find them anymore.
> 
> 

Yes, I agree with you. 
But the dummies are added to simple residues and 
there is no bonded interaction with them.
And the atom types are also correct.

It really should work...

And if I set them to the bottom of the protein, it works.
(...but then they are not in the charge-group I want them to be)



Frank