17 March 2016 8 9K Report

Dear Gromacs users,

I'm trying to calculate the distance between two specific residues of the active site of my protein in MD. I have made separate .index file of two specific groups. Then I am trying this command

" gmx distance -f md_0_1.xtc -s md_0_1.tpr -oav distance.xvg -select -n index.ndx -to ns ". When I am selecting my residues numbers for option -select in the above command. an error appeared that pairs are not found in your selection residues (1st residue "11 atoms" and 2nd residue "15 atoms" ). Kindly guide me on how I calculate the distance between two specific residues in MD.

Thanks,

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