[gmx-users] error in running g_dist

Arunima Shilpi writetoash28 at gmail.com
Wed May 22 11:53:47 CEST 2013

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

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