[gmx-users] Distance between two specific residues

Abid Channa abid_channa04 at yahoo.com
Thu Mar 17 05:01:08 CET 2016

Dear Gromacs users,
I am trying to calculate distance between two specific residues of 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 -tu ns ". When I am selecting my residues numbers for option -select in above command. error  appeared that pairs are not found in your selection residues (1st residue "11 atoms" and 2nd residue "15 atoms" ). Kindly guide me how I calculate distance between two specific residues in MD.
Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
 Dr .Panjwani Center for Molecular Medicine and Drug Research (PCMD),
 International Center for Chemical and Biological Sciences  (ICCBS),
 University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292 Ext. (309)
             Cell # +923013553051.



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