I am trying to find the hydrogen bonds in an 81-residue protein. I am
using the ptraj script given below. I can't get the program to save the
hydrogen bond data to a file. The data is printed on the screen but will
not go into a file. Can someone look at my script and tell me what I
need to do to get the hbond information to go to hbond.dat?
Thanks!
John
ptraj file.prmtop << EOF
trajin file 1.mdcrd
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 list
hbond distance 3.5 angle 120.0 donor acceptor includeself print series
hb.out
EOF
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Received on Mon Jun 28 2010 - 05:00:06 PDT
