Hi guys I have a problem with one module of my script. It's awk script running in pbs file - It's working when I make a call from pbs to separate awk only file like this
Quote:
awk -f OW-out.awk <snapshot0.pdb>OW-snap0
but when I try to execute this code in pbs file it fails
Code:
awk 'BEGIN { max = -1000; min = 1000 }
{
{$4 == "TCO"}
{value = $5 ~ /^[[:alpha:]]$/ ? $9 : $8;
max = max < value ? value : max;
min = min > value ? value : min;
$3 == "OW" && ($8 >min && $8 <max || $8 == min || $8 == max )} {print NR, $2, $3, $5, $6, $7, $8}
}' snap0.pdb>snap0-OW
It executes only this command
Code:
{print NR, $2, $3, $5, $6, $7, $8}
Here#s example of input
Code:
ATOM 4685 HB1 PRO A 322 23.988 40.451 115.223 1.00 0.00
ATOM 4686 HB2 PRO A 322 25.018 39.501 116.373 1.00 0.00
ATOM 4687 CG PRO A 322 22.858 39.661 116.803 1.00 0.00
ATOM 4688 HG1 PRO A 322 21.968 39.931 116.223 1.00 0.00
ATOM 4689 HG2 PRO A 322 22.878 38.581 116.893 1.00 0.00
ATOM 4690 CD PRO A 322 22.728 40.201 118.313 1.00 0.00
ATOM 4691 HD1 PRO A 322 21.718 40.511 118.563 1.00 0.00
ATOM 4692 HD2 PRO A 322 23.008 39.401 119.013 1.00 0.00
ATOM 4693 C PRO A 322 23.858 42.771 116.393 1.00 0.00
ATOM 4694 O1 PRO A 322 24.688 43.721 116.293 1.00 0.00
ATOM 4695 O2 PRO A 322 22.628 42.691 115.973 1.00 0.00
ATOM 4696 C1 TCO B 323 90.664 64.841 42.383 1.00 0.00
ATOM 4697 C2 TCO B 323 90.074 64.211 65.623 1.00 0.00
ATOM 4698 C3 TCO B 323 89.624 62.731 65.433 1.00 0.00
ATOM 4699 C4 TCO B 323 88.894 62.251 166.673 1.00 0.00
ATOM 4700 C5 TCO B 323 88.634 60.761 166.523 1.00 0.00
ATOM 4701 C6 TCO B 323 88.114 60.131 167.803 1.00 0.00
ATOM 4702 O7 TCO B 323 88.854 59.851 168.753 1.00 0.00
ATOM 46103 HW1 SOL 7981 30.758 -0.449 19.783 1.00 0.00
ATOM 46104 HW2 SOL 7981 31.818 0.771 19.533 1.00 0.00
ATOM 46105 OW SOL 7982 15.138 42.461 20.343 1.00 0.00
ATOM 46106 HW1 SOL 7982 15.858 42.321 21.013 1.00 0.00
ATOM 46107 HW2 SOL 7982 15.178 41.731 19.663 1.00 0.00
ATOM 46108 OW SOL 7983 63.308 14.411 0.803 1.00 0.00
ATOM 46109 HW1 SOL 7983 63.438 15.351 0.483 1.00 0.00
ATOM 46110 HW2 SOL 7983 63.988 13.811 0.383 1.00 0.00
ATOM 46111 OW SOL 7984 12.378 9.411 91.843 1.00 0.00
ATOM 46112 HW1 SOL 7984 12.948 8.621 92.073 1.00 0.00
ATOM 46113 HW2 SOL 7984 12.158 9.911 92.683 1.00 0.00
ATOM 46114 OW SOL 7985 9.468 59.311 104.643 1.00 0.00
ATOM 46115 HW1 SOL 7985 8.768 59.691 105.253 1.00 0.00
ATOM 46116 HW2 SOL 7985 10.368 59.681 104.903 1.00 0.00
ATOM 46117 OW SOL 7986 4.488 32.241 44.263 1.00 0.00
ATOM 46118 HW1 SOL 7986 4.308 31.791 45.143 1.00 0.00
ATOM 46119 HW2 SOL 7986 3.738 32.871 44.063 1.00 0.00
ATOM 46120 OW SOL 7987 64.378 17.281 231.638 1.00 0.00
ATOM 46121 HW1 SOL 7987 64.078 18.161 231.278 1.00 0.00
ATOM 46122 HW2 SOL 7987 65.288 17.371 232.028 1.00 0.00
ATOM 46123 OW SOL 7988 21.098 12.041 64.393 1.00 0.00
ATOM 46124 HW1 SOL 7988 21.628 12.571 63.743 1.00 0.00
ATOM 46125 HW2 SOL 7988 21.648 11.851 65.203 1.00 0.00
ATOM 46126 OW SOL 7989 89.154 23.561 223.108 1.00 0.00
ATOM 46127 HW1 SOL 7989 88.994 22.571 223.118 1.00 0.00
ATOM 46128 HW2 SOL 7989 90.094 23.751 222.838 1.00 0.00
ATOM 46129 OW SOL 7990 18.518 62.281 68.303 1.00 0.00
ATOM 46130 HW1 SOL 7990 19.398 62.621 67.953 1.00 0.00
ATOM 46131 HW2 SOL 7990 18.678 61.771 69.153 1.00 0.00
ATOM 46132 OW SOL 7991 82.328 54.771 23.723 1.00 0.00
ATOM 46133 HW1 SOL 7991 81.528 54.791 23.123 1.00 0.00
ATOM 46134 HW2 SOL 7991 83.138 54.531 23.183 1.00 0.00
ATOM 46135 OW SOL 7992 14.968 30.861 133.363 1.00 0.00
ATOM 46136 HW1 SOL 7992 15.528 31.181 132.603 1.00 0.00
ATOM 46137 HW2 SOL 7992 15.548 30.471 134.083 1.00 0.00
ATOM 46138 OW SOL 7993 2.928 50.331 47.593 1.00 0.00
ATOM 46139 HW1 SOL 7993 3.828 50.241 47.173 1.00 0.00
ATOM 46140 HW2 SOL 7993 2.428 49.471 47.493 1.00 0.00
ATOM 46141 OW SOL 7994 24.828 65.181 253.138 1.00 0.00
ATOM 46142 HW1 SOL 7994 24.738 64.991 252.168 1.00 0.00
ATOM 46143 HW2 SOL 7994 24.078 64.741 253.638 1.00 0.00
ATOM 46144 OW SOL 7995 29.148 19.901 135.113 1.00 0.00
ATOM 46145 HW1 SOL 7995 28.678 19.251 135.713 1.00 0.00
ATOM 46146 HW2 SOL 7995 29.698 20.521 135.663 1.00 0.00
ATOM 46147 OW SOL 7996 45.958 2.891 59.383 1.00 0.00
ATOM 46148 HW1 SOL 7996 46.428 3.661 58.953 1.00 0.00
Thanks for Your time!
Take care,
grincz
Last edited by pludi; 03-08-2012 at 03:34 AM..
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