AMBER Archive (2006)

Subject: Re: AMBER: hbond analysis

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Oct 03 2006 - 11:35:32 CDT

Hi Tom,

Thanks ... I was afraid that this is the only way. Carnal has a nice way
to do this (see script below)... Maybe sometime in the future, you'll be
interested to add such a feature to ptraj also.

Cheers
vlad

FILES_IN
 PARM p a.top;
 STREAM s a.mdcrd;
FILES_OUT
 HBOND hb Hbonds TABLE LIST;
DECLARE
 GROUP d ((ATOM NAME NZ N NE NH1 NH2 ND2 OG1) &
  (RES 47,76,78-84,94,192,193,216,260,264,268,336,361,468));
OUTPUT
 HBOND hb DONOR d DISTANCE 3.2 ANGLE 60.0 STATS;
END
EOF

Thomas Cheatham wrote:

>>Thanks for answering but the "acceptor" has nothing to do with waters.
>>The mask :1-467_at_O* means all possible oxygens in the protein itself.
>>
>>
>
>OK, then you need to make sure that there is a 1-1 mapping between oxygens
>and hydrogens in the selections. The easiest way to do this is NOT to use
>the mask but to explicitly pick them for each residue. Although tedious
>the first time, you can re-use the script....
>
>acceptor SER OG HG
>acceptor THR OG1 HG1
>
>--tom
>
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-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/

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