atom select within hbond analysis

From: Branko (
Date: Tue Jun 07 2011 - 07:40:09 CDT

Dear NAMD users,

This is more VMD question, but I was unsubscribe from vmd-l few months
ago. Briefly, please let me know what is correct syntax for
specification of atoms for which Hbond should be calculated using
Extension/Analysis/Hydrogen bonds.
I need to calculate distance between particular carbonyl oxygen and
carboxyl -OH for whole trajectory, so I specified "index 7 17", also
try with "name O8 O18", same with braces (index 7 17) and so on but
script could not parse selection. Thanks for advise


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