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 53 atom in pdb file, i couldn't get
segmentation fault.
Here is the my 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
END
Can you help me to solve this problem
Any suggestion is appreciated.
Thank you in advance
with regards,
Nagaraju.
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pg1.pdb
Description: 3877521777-pg1.pdb
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