[AMBER] hydrogen bond printout

From: Beale, John <John.Beale.stlcop.edu>
Date: Thu, 1 Jul 2010 06:29:14 -0500

My input file to the ptraj hbond suite looks like this:


ptraj file1.prmtop << EOF

trajin file2.nc

donor mask :1-81.O

donor mask :1-81.N

donor ASP OD1

donor ASP OD2

donor GLU OD1

donor GLU OD2

acceptor LYS N H


acceptor SER OG HG

hbond distance 3.0 angle 120.0 donor acceptor includeself series hb out



When I run the script, the proper hb.out file is generated. I have a
couple of questions about this file.



What does the string of characters (e.g.
.@@@*@@**@@*@............................) in the hydrogen bond printout
mean? I know that the characters ".,*,x,o,-, and ." refer to percentage
occupancy of the particular hydrogen bond. There are 46 such characters
at the end of the line that gives the hydrogen bonding data for two
H-bonded residues in the protein. Where did that number of 46 come from?


Also- the hydrogen bond printout has the following columns:


                                lifetime maxocc

         17.6 ( 12.8) 47

         14.0 ( 14.6) 53



What do these numbers mean?






John M. Beale, Jr., Ph,D.

Professor of Medicinal Chemistry and Pharmacognosy

St. Louis College of Pharmacy

4588 Parkview Place

St. Louis, Missouri 63110


Cell: (314)-315-0409

FAX (314) 446-8460







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Received on Thu Jul 01 2010 - 04:30:09 PDT
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