[gmx-users] Dummy atoms

[Anton Feenstra]

> 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
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|        | Anton Feenstra                                            |
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