[gmx-users] Dummy atoms

Anton Feenstra feenstra at chem.vu.nl
Fri Apr 5 14:02:47 CEST 2002


> Sergio Oyama Junior wrote:
> 
> Dear all,
> 
> When I manually insert dummy atoms into my topology file, grompp
> returns the following message:
> 
> Fatal error: [ file "tx4.top", line 615 ]:
>                  Atom index (595) in dummies2 out of bounds (1-593)
> 
> Can you please advise me how to correct it?

It seems pretty obvious to me: you refer to a non-existent atom number.
You should be aware that the definitions you give in a [ dummies* ]
section in your .top does not create an additional atom, you first
need to define the dummy atom also in the [ atoms ] section, and then
define a [ dummies* ] entry...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "Clickety Clickety Click" (System Manager From Hell)      |
|________|___________________________________________________________|



More information about the gromacs.org_gmx-users mailing list