From: Amor San Juan (
Date: Sun Nov 07 2010 - 23:32:20 CST

Hi all,

I hope to receive feedback in regard to this issue.

I issued the command:

same residue as (within 5 of resid 188-199)

The command above has selected nearby residues at 5 angstrom distance from a peptide (resid 188-199). My input was a trajectory file. The output desired is also a trajectory including residues nearest to the peptide.

The output shows complete structure of residue. The problem I face is how to add a terminal carbonyl oxygen to each selected residues ? I understand that vmd is a molecular viewer not an editor, but I want to know if there is a way for this task to be achieved by using it.

Thank You.