[gmx-users] Topology and co-ordinates do not match

[Natalie Tatum]

Hi Peter,

Deleting this lines appears to have worked and I've progressed through to
minimising the complex. THANK YOU. I don't think I would ever have spotted
that on my own!

Natalie

On 20 September 2017 at 12:54, Peter Kroon <p.c.kroon at rug.nl> wrote:

> Hi Natalie,
>
>
> I think the problem is your GMX_DRG.itp defines a [system] and
> [molecules] section containing a DRG molecule at the bottom.
>
>
> Peter
>
>
> On 20-09-17 13:45, Natalie Tatum wrote:
> > Hi Peter,
> >
> > Yes. The protein is 4600 atoms, I edited to 4647 to account for the
> ligand
> > of 47 atoms at the end of the gro file. The ligand is carried through
> into
> > the subsequent co-ordinate files, but as soon as I hit grompp I have an
> > issue.
> >
> > Natalie
> >
> > On 20 September 2017 at 12:42, Peter Kroon <p.c.kroon at rug.nl> wrote:
> >
> >> Hi Natalie,
> >>
> >>
> >> did you change the particle count on the second line of your gro file?
> >>
> >>
> >> Peter
> >>
> >>
> >> On 20-09-17 13:31, Natalie Tatum wrote:
> >>> Dear all,
> >>>
> >>> I have what appears to be a common problem but I can't seem to track
> down
> >>> the solution. The number of coordinates in my coordinate file
> >>> (complex_solvated.gro, 73587, does not match topology (topol.top,
> 73634).
> >>> This is of course a difference of 47 atoms, the precise number in my
> >> ligand.
> >>> As far as I can tell, I have correctly appended my ligand.gro to my
> >>> complex.gro, changing the corresponding header +47, and this is carried
> >>> through to complex_solvated.gro. The numbers at the bottom of topol.top
> >> sum
> >>> to match the co-ordinate file (22980*3 + 4600+47).
> >>>
> >>> So, I'm honestly not sure how this error is (a) coming about and (b)
> can
> >> be
> >>> solved. I'm thinking perhaps the topology isn't correctly including the
> >>> ligand topology, but I have placed that in the topol.top correctly as
> far
> >>> as I can see. The ligand topology was created in Antechamber and
> >> converted
> >>> with ACPYPE.
> >>>
> >>> Relevant files are here:
> >>>
> >>> complex.gro: https://drive.google.com/open?id=0B8FqO1m_a-
> >> iGSXVYTW5qQk1rSUE
> >>> complex_solvated.gro:
> >>> https://drive.google.com/open?id=0B8FqO1m_a-iGem02WGlQWWlDS0U
> >>>
> >>> DRG_GMX.gro: https://drive.google.com/open?id=0B8FqO1m_a-
> >> iGUVZ3eFZieEtiRUE
> >>> DRG_GMX.itp: https://drive.google.com/open?id=0B8FqO1m_a-
> >> iGS19wSVAySlhaTVk
> >>> topol.top: https://drive.google.com/open?id=0B8FqO1m_a-
> iGSWlQMnhSUm15b3c
> >>>
> >>> Can anyone shed light on where I'm going wrong?
> >>>
> >>> Much appreciated,
> >>>
> >>> Natalie
> >>>
> >>>
> >>>
> >>>
> >>> ----
> >>>
> >>> Dr. Natalie J. Tatum
> >>> PDRA | NICR, Newcastle University
> >>
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/
> >> Support/Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
> >
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
*Dr. Natalie J. Tatum*
Post-doctoral Research Associate
Northern Institute for Cancer Research
Newcastle University