AMBER Archive (2009)

Subject: Re: [AMBER] HB for each snapshot

From: Jason Swails (jason.swails_at_gmail.com)
Date: Wed Nov 04 2009 - 13:35:07 CST

Marcin,

Professor Carlson's group at the University of Michigan develops
python-based analysis tools that I believe may be able to help with this
issue (specifically PyPAT for H-bonding). You can find her resources at
http://sitemaker.umich.edu/carlsonlab/resources.html . I hope this helps,
and thanks to Professor Carlson for making these tools publicly available.
There is also thorough documentation included with the download.

Good luck!
Jason

2009/11/4 Marcin Krol <mykrol_at_cyf-kr.edu.pl>

> Hello,
>
> A couple of weeks ago I asked whether ptraj can tell me the presence or
> absence of HB for each snapshot of a trajectory between a given pair of
> residues. Using hbond facility I can get occupancy and a graphical
> representation showing schematic of time-series, but what I really need is
> the HB information for each snapshot. I'm sure ptraj generates this info (to
> get the occupancy, etc), but I don't know how to get it. Please let me know
> i if I can get _per snaphot_ analysis of HBs in ptraj, it'll save me lots of
> work.
>
> Or maybe you can suggest another program to perform such analysis. Any help
> appreciated
>
> Thanks in advance
> best
> Marcin
>
> --
> Dr Marcin Krol
> Zaklad Bioinformatyki i Telemedycyny
> Collegium Medicum Uniwersytet Jagiellonski
> e-mail: mykrol_at_cyf-kr.edu.pl
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber