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

D. Ensign densign at stanford.edu
Wed May 3 03:09:19 CEST 2006


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

; 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

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.

What might be going on here?

Frustrated enough to throw things, but not hard enough to spill my beer,
Dan Ensign
Stanford University
"Give up learning, and put an end to your troubles." -- Lao Tzu

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