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

[Peter Kroon]

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