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

[Yang Ye]

Try this:

1. Paste this at the place of my_ions.itp to replace it.

[ moleculetype ]
 NA+             1
 [ atoms ]
1       amber99_31  1       NA+             NA+      1      1    22.99000
[ moleculetype ]
CL-             1
[ atoms ]
1       amber99_30  1      CL-             CL-       1      -1   35.45000

2. Replace "Ions  1" with

Na+ 6
Cl- 2

Good luck.

Regards,
Yang Ye
D. Ensign wrote:
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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
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