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

[Natalie Tatum]

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




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Dr. Natalie J. Tatum
PDRA | NICR, Newcastle University