[gmx-users] Topology and co-ordinates do not match
nataliejtatum at gmail.com
Wed Sep 20 13:31:51 CEST 2017
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
Relevant files are here:
Can anyone shed light on where I'm going wrong?
Dr. Natalie J. Tatum
PDRA | NICR, Newcastle University
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