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

[Natalie Tatum]

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