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

[Jennifer Vo]

Dear All,
Sorry for pasting the *.gro file instead of topology. Here is the topology
[ moleculetype ]
; Name   nrexcl
NAP      3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1    OA    1    NAP     O3X    1   -0.796  15.9994
    2     H    1    NAP    HOP3    1    0.297   1.0080
    3 P, SI    1    NAP     P2B    1    2.683  30.9738
    4    OM    1    NAP     O1X    1   -1.000  15.9994
    5    OA    1    NAP     O2B    1   -0.685  15.9994
    6    OA    1    NAP     O2X    1   -0.796  15.9994

It starts from 1 as well. Many thanks for any help.
Regards,
Jennifer

On Fri, Jan 23, 2015 at 5:13 PM, Jennifer Vo <quyviolet at gmail.com> wrote:

> Dear All,
> I have got this error after running grompp
> Fatal error:
> Atoms in the .top are not numbered consecutively from 1 (rather, atomnr =
> 4, while at->nr = 2)
>
> My topology file is
> ; Include forcefield parameters
> #include "gromos54a7.ff/forcefield.itp"
>
> ; Include ligand topology
> #include "nap_uniatom.itp"
>
> ; Include water topology
> #include "gromos54a7.ff/spc.itp"
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> [ system ]
> ; Name
> NAP in water
> [ molecules ]
> ; Compound        #mols
> NAP                   1
> SOL              2654
>
> The I checked the file "nap_uniatom.itp" and it start from Atom 1,
> NAP
>  8026
>     1NAP    O3X    1   2.599   2.617   1.841
>     1NAP   HOP3    2   2.518   2.642   1.886
>     1NAP    P2B    3   2.654   2.469   1.866
>     1NAP    O1X    4   2.628   2.363   1.772
>     1NAP    O2B    5   2.580   2.447   2.009
>     1NAP    O2X    6   2.802   2.504   1.908
>     1NAP   HOP2    7   2.817   2.591   1.946
>
> Could you please tell me where is the problem from and a possible solution?
>  Many thanks in advance.
> Regards,
> Jennifer
>