[gmx-users] Creating index group of residues by vicinity to ligand

Mark Abraham Mark.Abraham at anu.edu.au
Sun Nov 22 09:37:27 CET 2009

shayamra at post.tau.ac.il wrote:
> Dear Gromacs Users,
> I am running a protein-ligand simulation in which the ligand interacts 
> with great a number of protein-residues ( > 30 ).
> In the interest of analysis I want to create an index group to include 
> *all* residues that are found in a certain cutoff (let us say 6A) from 
> the surface of my ligand, and do this throughout the entire simulation.
> Can anyone give me some pointers as which Gromacs commands may help?

Check out g_dist.


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