[gmx-users] fatal error in minimization

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jun 12 09:11:33 CEST 2008

Anamika Awasthi wrote:
> Dear Friends,
>         I extracted few conformation from my running job by using 
> trjconv. but now as I want to minimize this conformation it is showing 
> Fatal error that  *.pdb  and *.top coordinates does not match.

Well that means they don't match. To see why, check you're using the 
right .top, and then go back and look at what you did with how you wrote 
your trajectory and then what you did with trjconv.

>          I gave this command for my minimization grompp -f em.mdp -c 
> *.pdb -o em.tpr -p *.top


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