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Bug #152

sigmentation fault while creating index file

Added by nagaraju mulpuri over 12 years ago. Updated over 12 years ago.

Status:
Closed
Priority:
Low
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Dear gmx users,
I am trying to make index file for POPG lipid molecule using the
command:
make_ndx -f popg.pdb -o index.ndx

I am getting segmentation fault, but when i am removing 53rd atom in pdb file,
i couldn't get segmentation fault.

Here is the POPG.pdb file

CRYST1 95.707 94.861 66.625 90.00 90.00 90.00 P 1 1
ATOM 1 H1 POP X 105 10.938 52.622 28.322 1.00 0.00
ATOM 2 O2 POP X 105 11.136 51.689 27.991 1.00 0.00
ATOM 3 H3 POP X 105 13.355 49.287 26.361 1.00 0.00
ATOM 4 C4 POP X 105 12.324 51.353 28.740 1.00 0.00
ATOM 5 C5 POP X 105 13.345 50.760 27.748 1.00 0.00
ATOM 6 C6 POP X 105 14.540 50.008 28.377 1.00 0.00
ATOM 7 O7 POP X 105 15.505 49.737 27.342 1.00 0.00
ATOM 8 P8 POP X 105 15.412 48.147 27.021 1.00 0.00
ATOM 9 O9 POP X 105 16.670 47.732 26.346 1.00 0.00
ATOM 10 O10 POP X 105 14.704 47.425 28.125 1.00 0.00
ATOM 11 O11 POP X 105 14.315 48.209 25.838 1.00 0.00
ATOM 12 C12 POP X 105 14.699 48.774 24.379 1.00 0.00
ATOM 13 C13 POP X 105 13.870 47.852 23.484 1.00 0.00
ATOM 14 O14 POP X 105 12.490 47.845 23.905 1.00 0.00
ATOM 15 C15 POP X 105 11.909 47.553 25.091 1.00 0.00
ATOM 16 O16 POP X 105 12.358 46.538 25.622 1.00 0.00
ATOM 17 C17 POP X 105 10.478 48.058 25.332 1.00 0.00
ATOM 18 C18 POP X 105 9.679 48.126 24.025 1.00 0.00
ATOM 19 C19 POP X 105 8.281 48.663 24.315 1.00 0.00
ATOM 20 C20 POP X 105 7.511 48.707 22.993 1.00 0.00
ATOM 21 C21 POP X 105 7.127 47.329 22.432 1.00 0.00
ATOM 22 C22 POP X 105 6.557 47.739 21.070 1.00 0.00
ATOM 23 C23 POP X 105 5.528 46.767 20.485 1.00 0.00
ATOM 24 C24 POP X 105 5.042 47.189 19.096 1.00 0.00
ATOM 25 C25 POP X 105 4.171 46.573 18.209 1.00 0.00
ATOM 26 C26 POP X 105 3.486 45.253 18.577 1.00 0.00
ATOM 27 C27 POP X 105 2.655 44.672 17.423 1.00 0.00
ATOM 28 C28 POP X 105 1.320 45.380 17.178 1.00 0.00
ATOM 29 C29 POP X 105 0.746 44.713 15.921 1.00 0.00
ATOM 30 C30 POP X 105 -0.598 45.308 15.514 1.00 0.00
ATOM 31 C31 POP X 105 -1.589 44.267 14.980 1.00 0.00
ATOM 32 C32 POP X 105 14.571 46.507 23.290 1.00 0.00
ATOM 33 O33 POP X 105 14.235 45.797 22.094 1.00 0.00
ATOM 34 C34 POP X 105 13.088 45.067 22.021 1.00 0.00
ATOM 35 O35 POP X 105 12.726 44.440 23.010 1.00 0.00
ATOM 36 C36 POP X 105 12.630 44.720 20.603 1.00 0.00
ATOM 37 C37 POP X 105 11.101 44.761 20.519 1.00 0.00
ATOM 38 C38 POP X 105 10.741 43.899 19.295 1.00 0.00
ATOM 39 C39 POP X 105 9.217 44.009 19.183 1.00 0.00
ATOM 40 C40 POP X 105 8.778 43.609 17.771 1.00 0.00
ATOM 41 C41 POP X 105 7.298 43.725 17.407 1.00 0.00
ATOM 42 C42 POP X 105 7.075 43.386 15.931 1.00 0.00
ATOM 43 C43 POP X 105 5.606 43.539 15.546 1.00 0.00
ATOM 44 C44 POP X 105 5.419 42.951 14.141 1.00 0.00
ATOM 45 C45 POP X 105 3.940 43.095 13.753 1.00 0.00
ATOM 46 C46 POP X 105 3.888 42.400 12.387 1.00 0.00
ATOM 47 C47 POP X 105 2.514 42.764 11.833 1.00 0.00
ATOM 48 C48 POP X 105 2.377 42.017 10.497 1.00 0.00
ATOM 49 C49 POP X 105 1.111 42.437 9.744 1.00 0.00
ATOM 50 C50 POP X 105 -0.239 42.030 10.343 1.00 0.00
ATOM 51 CA1 POP X 105 -2.690 44.707 14.004 1.00 0.00
ATOM 52 CA2 POP X 105 -2.007 45.289 12.769 1.00 0.00
ATOM 53 OA3 POP X 105 12.734 50.000 26.697 1.00 0.00
TER
END

History

#1 Updated by Erik Lindahl over 12 years ago

Works fine for me, tested both with 3.3.1 and development branch.

Also available in: Atom PDF