[gmx-users] Error regarding topology and coordinate files

Bharath K. Srikanth s.bharath at iitg.ernet.in
Wed Sep 12 20:38:04 CEST 2012


I am trying to run a simulation of the self-assembly of a course-grained
lipid bilayer using GROMACS. So far, I have made a box of DSPC lipid
molecules (7.5 x 7.5 x 7.5, 128 molecules). I have also added water
molecules using the genbox command (768 water molecules added), and named
the coordinate file as waterbox.gro.

For the next step, when I try to run a minimization, I get an error as

Fatal error:
number of coordinates in coordinate file (waterbox.gro, 2560)
             does not match topology (dspc.top, 1792)

What I understood from this was that the water molecules (768 water
molecules = 2560-1792) added by genbox had not been updated to the
topology file. However, my topology file reads as follows:

#include "martini_v2.1.itp"
#include "martini_v2.0_lipids.itp"

[ system ]

[ molecules ]
DSPC 128
; W 768

which indicates that 768 water molecules have, indeed, been added to the
topology file- this appears to be fine. Is there anything I'm missing out
on here?

Thanks a lot!

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