[gmx-users] Error in MD simulation

[Justin A. Lemkul]

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

-- 
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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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