AMBER Archive (2004)

Subject: AMBER: (No subject)

From: opitz_at_che.udel.edu
Date: Thu Jan 29 2004 - 16:09:47 CST

('binary' encoding is not supported, stored as-is) Hello Amber Community,

I am trying to read a pdb file into antechamber. Smaller files work find
and I get the prepin file etc. etc. A larger file I have that I need to
put into antechamber, it crashes. Here is the command and following error
message I get:

antechamber -i file.pdb -fi pdb -o file.prepin -fo prepi -s 2

 Unrecognized atomic name , exitSegmentation fault (cored dumped)

Does anyone know what causes my crash? Is it a problem in the number of
atoms that can be read into antechamber, and if so, where do I change
those limits?
Here ist the first few lines of the pdb file then continued around the
number of atoms where the crash usually happens (atom 513):

ATOM 4 N UNK 1 2.794 -5.632 1.628 1.00 0.00
ATOM 5 H UNK 1 2.867 -6.567 1.339 1.00 0.00
ATOM 6 C UNK 1 -2.310 -3.184 2.662 1.00 0.00
ATOM 7 H UNK 1 -1.466 -3.777 2.913 1.00 0.00
ATOM 8 H UNK 1 -2.077 -2.575 1.805 1.00 0.00
ATOM 9 C UNK 1 -2.660 -2.297 3.964 1.00 0.00
ATOM 10 H UNK 1 -1.875 -2.246 4.622 1.00 0.00
ATOM 11 H UNK 1 -3.423 -2.888 4.511 1.00 0.00
ATOM 12 N UNK 1 -3.068 -0.993 3.523 1.00 0.00
ATOM 13 C UNK 1 -1.634 1.117 3.822 1.00 0.00
ATOM 14 H UNK 1 -0.797 1.681 3.353 1.00 0.00
ATOM 15 H UNK 1 -1.255 0.804 4.780 1.00 0.00
ATOM 16 C UNK 1 -1.982 -0.108 3.020 1.00 0.00
ATOM 17 H UNK 1 -1.124 -0.705 2.845 1.00 0.00
ATOM 18 H UNK 1 -2.382 0.206 2.060 1.00 0.00
ATOM 19 C UNK 1 -2.919 2.027 4.082 1.00 0.00
ATOM 20 O UNK 1 -3.740 1.769 4.972 1.00 0.00
ATOM 21 C UNK 1 3.126 1.928 4.911 1.00 0.00
ATOM 22 H UNK 1 3.151 1.094 4.137 1.00 0.00
ATOM 23 H UNK 1 4.141 2.393 4.775 1.00 0.00
ATOM 24 C UNK 1 2.911 1.413 6.313 1.00 0.00
ATOM 25 H UNK 1 2.916 2.243 7.072 1.00 0.00
ATOM 26 H UNK 1 3.738 0.798 6.626 1.00 0.00
ATOM 27 N UNK 1 2.017 2.818 4.675 1.00 0.00
ATOM 28 H UNK 1 1.172 2.405 4.262 1.00 0.00
ATOM 29 N UNK 1 1.630 0.647 6.427 1.00 0.00
ATOM 30 H UNK 1 1.754 -0.298 6.116 1.00 0.00
ATOM 31 H UNK 1 0.764 1.119 6.017 1.00 0.00
ATOM 32 C UNK 1 1.898 4.084 4.818 1.00 0.00
ATOM 33 O UNK 1 2.863 4.752 5.164 1.00 0.00
ATOM 34 C UNK 1 0.140 4.808 3.187 1.00 0.00
ATOM 35 H UNK 1 0.075 3.741 2.866 1.00 0.00
ATOM 36 H UNK 1 0.883 5.274 2.630 1.00 0.00
ATOM 37 C UNK 1 0.453 4.685 4.650 1.00 0.00
ATOM 38 H UNK 1 -0.263 4.076 5.176 1.00 0.00
ATOM 39 H UNK 1 0.575 5.645 5.112 1.00 0.00

ATOM 500 H UNK 1 11.369 4.391 -2.747 1.00 0.00
ATOM 501 H UNK 1 10.814 2.919 -3.456 1.00 0.00
ATOM 502 C UNK 1 10.647 2.521 -0.689 1.00 0.00
ATOM 503 O UNK 1 9.513 2.535 -1.175 1.00 0.00
ATOM 504 N UNK 1 10.752 2.419 0.658 1.00 0.00
ATOM 505 H UNK 1 9.901 2.290 1.200 1.00 0.00
ATOM 506 C UNK 1 11.956 1.997 1.437 1.00 0.00
ATOM 507 H UNK 1 11.626 1.247 2.186 1.00 0.00
ATOM 508 H UNK 1 12.665 1.552 0.674 1.00 0.00
ATOM 509 C UNK 1 12.592 3.229 2.067 1.00 0.00
ATOM 510 H UNK 1 12.756 3.924 1.215 1.00 0.00
ATOM 511 H UNK 1 13.628 2.981 2.411 1.00 0.00
ATOM 512 N UNK 1 11.764 3.742 3.175 1.00 0.00
ATOM 513 H UNK 1 11.815 4.716 3.382 1.00 0.00
ATOM 514 H UNK 1 10.952 3.250 3.453 1.00 0.00
ATOM 515 C UNK 1 12.488 3.357 -5.274 1.00 0.00
ATOM 516 H UNK 1 11.906 4.308 -5.508 1.00 0.00
ATOM 517 H UNK 1 13.461 3.320 -5.713 1.00 0.00
ATOM 518 C UNK 1 11.528 2.240 -5.791 1.00 0.00
ATOM 519 H UNK 1 10.549 2.810 -5.698 1.00 0.00
ATOM 520 H UNK 1 11.452 1.295 -5.232 1.00 0.00
ATOM 521 N UNK 1 11.690 2.039 -7.232 1.00 0.00
ATOM 522 H UNK 1 11.213 2.752 -7.780 1.00 0.00
ATOM 523 N UNK 1 14.889 -3.231 -4.207 1.00 0.00
ATOM 524 H UNK 1 15.511 -4.029 -3.961 1.00 0.00
ATOM 525 C UNK 1 14.335 -2.825 -3.053 1.00 0.00
ATOM 526 O UNK 1 14.795 -3.281 -2.032 1.00 0.00
ATOM 527 C UNK 1 13.138 -1.819 -2.969 1.00 0.00
ATOM 528 H UNK 1 13.184 -1.126 -2.116 1.00 0.00
ATOM 529 H UNK 1 13.241 -1.173 -3.873 1.00 0.00
ATOM 530 C UNK 1 11.716 -2.536 -2.943 1.00 0.00

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