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.
http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
-Justin
Can anyone throw some light on what I've gone wrong!!
Thanks loads!
Natalie
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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