Arden Perkins wrote:
I am an undergraduate student and I am still learning to use GROMACS.
When I add my ions to the solution (using genion) by the procedure
described in the funnel web spider tutorial the .gro and .top files do
not match. I tried subtracting solvent molecules but they still dont
match and I can't continue. What am I doing wrong?
Hard to say. The bottom line is you haven't updated the topology correctly. If
you use the -p flag with genbox (when adding solvent) and genion (when adding
ions) the changes are made automatically and you don't have to worry about
troubleshooting :)
For information on the error:
http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
-Justin
Thanks!
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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