[gmx-users] error in running g_dist

[Mark Abraham]

Use gmxcheck to find out what's in the files. Think about how you used
xtcgroups. Consider using tpbconv to make a matching subset from your .tpr.

Mark


On Wed, May 22, 2013 at 11:53 AM, Arunima Shilpi <writetoash28 at gmail.com>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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