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

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 22 13:01:59 CEST 2010

Natalie Stephenson 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. 

Are you making manual updates, or allowing genbox/genion to make changes for 
you?  In the case of the former, check your work :)  In the case of the latter, 
I'd be more concerned.

There really is nothing diagnostic that can be done.  You simply have to check 
how many of each molecule are in your system.  Something has gone wrong 
somewhere along the way.



> Can anyone throw some light on what I've gone wrong!!
> Thanks loads!
> Natalie


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


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