Re: atom select within hbond analysis

From: sajad falsafi (
Date: Tue Jun 07 2011 - 09:21:09 CDT

Hi, you can not type 'atomtype' or 'index'. We suggest to type 'protein', 'chain X' or 'resid 1 to 20'. After words, in the "Calculation details info for:" part which contain different option you can select for observing more details information of Hbonds. Then you can see more details in output file. Hope this helps you. Sajad and Zahra

On Tue Jun 7th, 2011 5:10 PM IRDT Branko wrote:

>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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