[gmx-users] dummy atoms

[David van der Spoel]

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.


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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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