VMD-L Mailing List
From: Christine Horejs (christine.horejs_at_gmail.com)
Date: Mon Oct 12 2009 - 09:04:51 CDT
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Hi everybody,
I was editing a pdb-file using awk in Linux. Now I wanted to see the
structure in VMD, but looks like I have a format mistake now in the file. I
can see the beads, but they are all in one line, so the coordinates are
obviously not recognized.
Does anyone know, how to get the right format in awk for the following file
(the last two columns are only information for me and should not influence
the structure):
ATOM 0 BB SER 1 0 -31.958 -25.125 -11.061 1.00 0.00
-0.8 0
ATOM 1 BB GLY 1 1 -32.079 -26.085 -14.466 1.00 0.00
-0.4 0
ATOM 2 BB VAL 1 2 -36.455 -21.265 -15.792 1.00 0.00
4.2 0
ATOM 3 BB SER 1 3 -37.401 -20.877 -19.029 1.00 0.00
-0.8 0
ATOM 4 BB ALA 1 4 -42.701 -21.232 -18.584 1.00 0.00
1.8 0
ATOM 5 BB VAL 1 5 -47.498 -23.718 -18.979 1.00 0.00
4.2 0
ATOM 6 BB THR 1 6 -47.989 -24.426 -21.973 1.00 0.00
-0.7 0
ATOM 7 BB ALA 1 7 -46.376 -27.080 -22.868 1.00 0.00
1.8 0
ATOM 8 BB VAL 1 8 -44.852 -28.570 -20.796 1.00 0.00
4.2 0
ATOM 9 BB LYS 1 9 -44.441 -30.062 -17.397 1.00 0.00
-3.9 +
ATOM 10 BB PRO 1 10 -42.131 -31.447 -17.346 1.00 0.00
-1.6 0
ATOM 11 BB GLY 1 11 -38.465 -30.749 -17.931 1.00 0.00
-0.4 0
ATOM 12 BB THR 1 12 -35.631 -31.422 -16.009 1.00 0.00
-0.7 0
ATOM 13 BB ALA 1 13 -34.695 -30.832 -12.632 1.00 0.00
1.8 0
ATOM 14 BB VAL 1 14 -40.025 -30.314 -9.385 1.00 0.00
4.2 0
ATOM 15 BB THR 1 15 -42.222 -28.312 -10.836 1.00 0.00
-0.7 0
ATOM 16 BB ALA 1 16 -41.021 -24.641 -11.197 1.00 0.00
1.8 0
ATOM 17 BB VAL 1 17 -36.632 -20.649 -11.141 1.00 0.00
4.2 0
I am thankful for every information,
best wishes,
Christine
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