[gmx-users] error using grompp: number of coordinates in coordinate file does not match topology

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 27 12:31:17 CEST 2012

On 6/27/12 4:31 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I am going through the tutorial for membrane protein simulation which is
> offered by gromacs.
> I did everything just like it is described in the tutorial but when I want
> to do the minimization in Step 3 after packing the lipids around the
> protein I always get the error the
> "number of coordinates in coordinate file (system_inflated.gro, 9900)
>               does not match topology (topol.top, 3800)"
> I understand why it is like that because I just append the membrane to the
> protein file but how can I also change the topology file?

With a text editor.  The content of the [molecules] directive must always agree 
with the contents of the coordinate file, with respect to number of molecules 
and the order in which the molecules appear.  You likely need to add a line in 
this directive indicating the number of DPPC molecules, which appears to be 122 
(9900-3800 = 6100 = 122 * 50).



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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