[gmx-users] gmx select help

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Thu Feb 21 20:55:54 CET 2019

Hi all,

I am running the gmx select command to create a file with all my ligand molecules that are within  the cut-off distance specified from the COM of a protein residue as a function of time. Here is the command I am using:

gmx select -f traj2.gro -s protein.tpr -dt 100 -on index.ndx -select 'resname LIG and within 0.5 of res_com of resnr 183' -resnr number

The file currently outputs atom numbers for my ligand molecules. If I only wanted the resid of my ligands (as named in the trajectory file, e.g. resid 130 LIG) instead of the atom id  to be written, how would I do this?


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