Dear Mark, Thanks a lot for drawing my attention repeatedly to the atom indices I was choosing for making the index file. I chose the atoms using the command 'a O r1' thinking it'll choose the oxygen atom of residue 1. Instead to my surprise,all the oxygen atoms of all residues were selected. I then gave the command 'a O 1 &r1' which chose the exact atoms I wanted and then did the same thing for all other residues.My problem was solved.. Thanks a lot
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