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

[Mark Abraham]

Hi,

I think the use of "P, SI" as a type name is illegitimate, and as such all
bets are off. Please complain to the place you got this, and for yourself,
replace them with something more suitable for your phosphorus type.

Mark

On Fri, Jan 23, 2015 at 5:17 PM, Jennifer Vo <quyviolet at gmail.com> wrote:

> 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
> >
> --
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