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

[Yang Ye]

D. Ensign wrote:
>>>> 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!
>>     
>
> I know everyone will be relieved I have solved my problem. For the possibility of aid to
> those who come after who might run into this problem, I provide a solution.
>
> Recall, the problem was an error while running grompp that, "Atoms in the .top are not
> numbered consecutively from 1" after adding ions with genion. Before adding ions, (ie,
> after adding the solvent) everything worked just fine.
>
> The problem seemed that grompp doesn't like to find atoms after the solvent. 
>   
Putting ions in the last has always been a conventional way. Would you 
like to try my method mentioned in previous mail?
Yang Ye