On 4/25/12 12:45 PM, vinee2here wrote:
Hi all!!
I am running a MD simulation of a protein modelled by using modeller...and I
am getting an error in the grompp command.
The error reported was : Number of coordinates in coordinate file
(z_b4em.gro) does not match that of topology file (z.top). We are however
not able to run the nohup command because of the above mentioned error.
The link for em.mdp and the output obtained is :
http://s1064.photobucket.com/albums/u378/vinee2here/
Your help in resolving this issue would be highly appreciated.
The fatal error should have also printed a URL that you can follow to find this
information:
http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
The solution to that particular error is always the same - keep track of your
molecules better. Use of the -p flag with genbox and genion to allow the
programs to do the bookkeeping for you eliminates the majority of the problems.
-Justin
--
========================================
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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