AMBER Archive (2006)

Subject: Re: AMBER: Ptraj: Hbond time series

From: Chng Choon-Peng (choonpeng_at_cb.k.u-tokyo.ac.jp)
Date: Tue Jul 11 2006 - 18:56:20 CDT

Hi Zu Thur,

On 2006/07/12, at 0:19, Zu Thur Yew wrote:

> Hi,
>
> I would just like to ask if its possible for ptraj to output the H-
> bonds (as defined by the masks) that are present for each frame? I
> understand its possible to do so for the distances, but that would
> lack an angular criteria.
>
> Thanks!
>
> ZT
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    What I know is that you can also specify an angle criteria to the
hbond keyword
in a PTRAJ script:
hbond distance 3.0 angle 120.0 series prot_hbonds

Then, the output from running PTRAJ tells you the %occupancy of each
specified donor/acceptor pair.
Those with low occupancy means they are not present, but you have to
specify many pairs.
Maybe there is a way to specify all possible donor/acceptor pairs to
PTRAJ
that I am not aware of.
Anyone else with more experience on doing hbond analysis please advice.

regards,
Choon-Peng

--------------------------------
Choon-Peng CHNG
Doctoral Student (Yr 1)
Dept of Computational Biology, Grad Sch of Frontier Science
The University of Tokyo
Affiliated with
Lab. of Molecular Design (Prof KITAO Akio)
Room 107, Institute of Molecular and Cellular Biosciences
1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
Tel: +81 03-5841-1472
http://www.iam.u-tokyo.ac.jp/MolDes/indexE.html
---------------------------------

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