[gmx-users] grompp: Atoms in the .top are not numbered consecutively from 1

[Yang Ye]

D. Ensign wrote:
> Greetings.
>
> I'm having a lovely time with my old pal grompp, except for the grumpiness after replacing
> eight water molecules with ions in my system and discovering -- to my astonishment -- the
> following message:
>
> "Atoms in the .top are not numbered consecutively from 1"
>
> Well, this is interesting, seeing as how it's preventing me from advancing, so is
> garnering all my attention. So I have a look at my topol.top, and I discover the
> following:
>
> ; BEGIN
> ; Topology for human aldose reductase with NAD+ and inhibitor
>
> ; Include force field
> #include "ffamber99.itp"
>
> ; Include protein topology
> #include "haldr.itp"
>
> ; Include inhibitor topology
> #include "inh1.itp"
>
> ; Include NAD+ topology
> #include "nad.itp"
>
> ; Include water topology
> #include "ffamber_tip3p.itp"
>
> #include "my_ions.itp"
>
> [ system ]
> hAldR with inhibitor in water
>
> [ molecules ]
> ;molecule name  number
> AldoseReductase 1
> Inhibitor1      1
> NAD             1
> SOL             27048
> ;SOL             27056
> Ions            1
> ;END
>
> Now, the odd thing is, when I comment out references to the Ions molecule and my_ions.itp,
> and remove the ions from the .gro file, everything works just fine! (Well, it works fine
> enough.) That's odd because I haven't treated the ion atoms in my_ions.itp any
> differently than I treated the atoms in Inhibitor1 or in NAD, other than they're after
> the water.
>
>   
paste your my_ions.itp here?
> What might be going on here?
>
> Frustrated enough to throw things, but not hard enough to spill my beer,
> Dan Ensign
> Stanford University
>   
Yang Ye