Hi John,
Try something like
ptraj prmtop < ptraj_script > output
Emmanuel
On Mon, Jun 28, 2010 at 5:54 AM, Beale, John <John.Beale.stlcop.edu> wrote:
> 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 - 08:30:04 PDT
