[gmx-users] Re: error in running g_dist

[Andrish Reddy]

Arunima Shilpi-2 wrote
> Respected sir
> 
> I want to calculate the distance between protein and ligand after I  have
> run the production step. I used the following command..
> 
> g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx
> 
> Groups I selected was
> Group 1 (protein)
> Group 13 (ligand)
> 
> It says the following error
> 
> Molecule in topology has atom numbers below and above natoms (11793).
> You are probably trying to use a trajectory which does not match the first
> 11793 atoms of the run input file.
> 
> how to debug the error...
> 
> -- 
> 
> Thanking You with Regards.
> 
> Arunima Shilpi
> 
> Ph. D Research Scholar(Cancer & Epigenetics)
> Department of Life Science
> National Institute of Technology
> Rourkela
> Odisha
> -- 
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Did you check that this "You are probably trying to use a trajectory which
does not match the first
11793 atoms of the run input file." is not the case?

Andrish



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