[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
hb.out

EOF

 

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?

 

Thanks!

 

John

 

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

Professor of Medicinal Chemistry and Pharmacognosy

St. Louis College of Pharmacy

4588 Parkview Place

St. Louis, Missouri 63110

(314)-446-8461

Cell: (314)-315-0409

FAX (314) 446-8460

jbeale.stlcop.edu

 

 

 

 

 

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