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
