[AMBER] (no subject)

From: Beale, John <John.Beale.stlcop.edu>
Date: Mon, 28 Jun 2010 06:54:02 -0500

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?






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





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Received on Mon Jun 28 2010 - 05:00:06 PDT
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