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

shayamra at post.tau.ac.il shayamra at post.tau.ac.il
Sun Nov 22 09:04:29 CET 2009

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?


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