AMBER Archive (2008)

Subject: Re: AMBER: Number of Hydrogen Bonds?

From: Jack Lei (leiming72_at_gmail.com)
Date: Fri Jan 25 2008 - 07:20:53 CST

You could compile a C/Perl/Python program to analysis the output file
generated
by carnal or ptraj.

Jack

On Jan 25, 2008 9:35 AM, <Jiapu.Zhang_at_csiro.au> wrote:

> Dear Amber friends,
>
> I am also caring about this subject, with one addition: the number of
> HBs of the protein with the WATs.
>
> Best regards,
> Jiapu
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of d90223013_at_ntu.edu.tw
> Sent: Friday, 25 January 2008 12:08
> To: amber_at_scripps.edu
> Subject: AMBER: Number of Hydrogen Bonds?
>
> Dear all,
> Does anyone know how to calculate "the number of hydrogen bonds" vs.
> "time" using ptraj ? As far as I know that ptraj is able to track the
> interactions between a list of hydrogen bond "donors" and hydrogen
> bond "acceptors" that the user specifies. However, it only reveals the
> maximum occupancy and lifetimes of a particular H-bond related to the
> time series when the option "series hbt" is added to the command line.
> Thank you for your help!
>
> Dr. Yi-Ming Cheng
>
> ========================
> Department of Chemistry,
> National Taiwan University
> personal site: http://mx.nthu.edu.tw/~ymcheng/>
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