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

[D. Ensign]

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> > 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?
> Yang Ye

As requested, kind person, here is my ions topology include file:

; BEGIN
[ moleculetype ]
; Name            nrexcl
Ions                   3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB     
massB
     1 amber99_31      1     Na     Na      1          1      22.99   ; qtot 1
     2 amber99_31      2     Na     Na      2          1      22.99   ; qtot 2
     3 amber99_31      3     Na     Na      3          1      22.99   ; qtot 1
     4 amber99_31      4     Na     Na      4          1      22.99   ; qtot 2
     5 amber99_31      5     Na     Na      5          1      22.99   ; qtot 2
     6 amber99_31      6     Na     Na      6          1      22.99   ; qtot 2
     7 amber99_30      7     Cl     Cl      7         -1      35.45   ; qtot 1
     8 amber99_30      8     Cl     Cl      8         -1      35.45   ; qtot -2
; END

For your comparison enjoyment, here is the .itp that I used as a guide for the template
above. This .itp was generated after I ran genion on a previous, less interesting system,
then ran pdb2gmx over again which built the .itp below. Unfortunately, running pdb2gmx in
the present case would be a bit of a pain, since I'm using GAFF parameters for my
inhibitor and the cofactor, and I want to mess with the ffamber99 files as little as
possible.

; BEGIN -- template itp file with ions that works, whereas the one above doesn't
[ moleculetype ]
; Name            nrexcl
Protein_B           3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB     
massB
     1 amber99_31      1     Na     Na      1          1      22.99   ; qtot 1
     2 amber99_31      2     Na     Na      2          1      22.99   ; qtot 2
     3 amber99_30      3     Cl     Cl      3         -1      35.45   ; qtot 1
     4 amber99_30      4     Cl     Cl      4         -1      35.45   ; qtot 0
     5 amber99_30      5     Cl     Cl      5         -1      35.45   ; qtot -1
     6 amber99_30      6     Cl     Cl      6         -1      35.45   ; qtot -2

; Include Position restraint file
#ifdef POSRES
#include "posre_B.itp"
#endif
; END -- template itp file that works.

I'm really wondering if having the ions after the solvent is what's messing this up -- in
the original case, the ions come after the solvent, whereas in the second case (the
template case) the ions come before the solvent in the gro and in the top.  Which means
I'll be spending a portion of the afternoon writing a Perl script! Woohoo!

Dan Ensign
Stanford University