[gmx-developers] dummy atoms

[K.A. Feenstra]

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?

When you renumber your atoms, you also have to renumber the
interaction (bond, angle etc.) defenitions, since these are
defined based on atom numbers. If the dummy atoms you insert
do not replace actual atoms, it is often best to simply place
them at the end of your topology to prevent renumbering.
THe only limiting factor are the charge groups; if you need
to have your dummy atom inside a specific charge group, it
must be at the proper place in the atoms list.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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