[gmx-users] Energy minimisation problems - coordinate file and topology file not matching.

Terry terrencesun at gmail.com
Wed Sep 22 12:55:25 CEST 2010

Hi, Natalie,

Obviously, number of coordinates still doesn't match the topology file even
you updated the topol.top *carefully*.
Check the topol.top thoroughly or paste several line of your coordinate and
topology files may be good ideas.

Note that the topology file is lacking information for *28* atoms. Does that
number remind you anything?


On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson <
Natalie.Stephenson at postgrad.manchester.ac.uk> wrote:

>  Hi everyone,
> I was hoping you could clear up a problem I'm having when performing energy
> minimisation.  I'm following the instructions from one of the tutorials
> (Justin's Umbrella Sampling) with my own protein, however, this time when I
> try to perform the energy minimisation it throws out this 'fatal error
> message' ...
>  number of coordinates in coordinate file (nrr_solv_ions.gro, 33181)
>              does not match topology (topol.top, 33153)
> I've been updating the topol.top file every time I've done something, so
> I'm not really sure what's happened.
> Can anyone throw some light on what I've gone wrong!!
> Thanks loads!
> Natalie
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