Dear Amber users,
I have tried leaprc.gcff force field for PEG to generate topology and
coordinate files but it gives me error that first three atoms are not
defined. could any one please help me how to fix it ?
Error message;
FATAL: Atom .R< 1>.A<H 1> does not have a type.
FATAL: Atom .R< 1>.A<O 2> does not have a type.
FATAL: Atom .R< 1>.A<C 3> does not have a type.
coordinates from pdb file
ATOM 1 H 1 16.667 16.667 16.667 0.00 1.00
H 0.0000
ATOM 2 O 1 16.685 16.550 17.594 3.07 1.00
O 0.0000
ATOM 3 C 1 15.466 15.899 17.883 3.40 1.00
C 0.0000
ATOM 4 H 1 15.593 15.384 18.868 2.47 1.00
H 0.0000
ATOM 5 H 1 15.213 15.177 17.064 2.47 1.00
H 0.0000
ATOM 6 C 1 14.522 17.057 17.896 3.40 1.00
C 0.0000
ATOM 7 H 1 14.829 17.769 18.628 2.47 1.00
H 0.0000
ATOM 8 H 1 13.599 16.718 18.228 2.47 1.00
H 0.0000
ATOM 9 O 1 14.425 17.768 16.675 3.00 1.00
O 0.0000
ATOM 10 C 1 13.351 18.612 16.851 3.40 1.00
C 0.0000
ATOM 11 H 1 13.467 19.123 17.824 2.47 1.00
H 0.0000
ATOM 12 H 1 12.377 18.188 16.782 2.47 1.00
H 0.0000
ATOM 13 C 1 13.448 19.727 15.707 3.40 1.00
C 0.0000
ATOM 14 H 1 14.439 19.900 15.300 2.47 1.00
H 0.0000
ATOM 15 H 1 13.021 20.619 16.216 2.47 1.00
H 0.0000
ATOM 16 O 1 12.471 19.455 14.734 3.00 1.00
O 0.0000
ATOM 17 C 1 12.169 20.621 14.075 3.40 1.00
C 0.0000
ATOM 18 H 1 13.112 21.068 13.685 2.47 1.00
H 0.0000
ATOM 19 H 1 11.711 21.371 14.715 2.47 1.00
H 0.0000
ATOM 20 C 1 11.164 20.415 12.973 3.40 1.00
C 0.0000
ATOM 21 H 1 10.714 21.405 12.769 2.47 1.00
H 0.0000
ATOM 22 H 1 10.412 19.703 13.312 2.47 1.00
H 0.0000
ATOM 23 O 1 11.896 19.896 11.798 3.00 1.00
O 0.0000
ATOM 24 C 1 11.054 19.825 10.616 3.40 1.00
C 0.0000
ATOM 25 H 1 10.483 20.763 10.463 2.47 1.00
H 0.0000
ATOM 26 H 1 10.268 19.055 10.895 2.47 1.00
H 0.0000
ATOM 27 C 1 11.808 19.372 9.368 3.40 1.00
C 0.0000
ATOM 28 H 1 12.374 20.176 8.953 2.47 1.00
H 0.0000
ATOM 29 H 1 11.021 19.025 8.694 2.47 1.00
H 0.0000
ATOM 30 O 1 12.645 18.290 9.625 3.00 1.00
O 0.0000
ATOM 31 C 1 13.223 17.954 8.398 3.40 1.00
C 0.0000
ATOM 32 H 1 12.497 17.812 7.602 2.47 1.00
H 0.0000
ATOM 33 H 1 13.929 18.694 7.965 2.47 1.00
H 0.0000
ATOM 34 C 1 13.924 16.578 8.498 3.40 1.00
C 0.0000
ATOM 35 H 1 14.294 16.228 7.506 2.47 1.00
H 0.0000
ATOM 36 H 1 13.411 15.776 8.975 2.47 1.00
H 0.0000
ATOM 37 O 1 15.217 16.737 9.214 3.00 1.00
O 0.0000
ATOM 38 C 1 15.914 15.527 9.338 3.40 1.00
C 0.0000
ATOM 39 H 1 16.042 15.010 8.362 2.47 1.00
H 0.0000
ATOM 40 H 1 15.344 14.861 10.008 2.47 1.00
H 0.0000
ATOM 41 C 1 17.327 15.739 9.961 3.40 1.00
C 0.0000
ATOM 42 H 1 18.009 15.110 9.518 2.47 1.00
H 0.0000
ATOM 43 H 1 17.737 16.731 9.766 2.47 1.00
H 0.0000
ATOM 44 O 1 17.312 15.595 11.343 3.00 1.00
O 0.0000
ATOM 45 C 1 16.430 16.534 11.911 3.40 1.00
C 0.0000
ATOM 46 H 1 16.672 17.534 11.637 2.47 1.00
H 0.0000
ATOM 47 H 1 15.349 16.409 11.677 2.47 1.00
H 0.0000
ATOM 48 C 1 16.580 16.545 13.480 3.40 1.00
C 0.0000
ATOM 49 H 1 15.888 17.285 13.823 2.47 1.00
H 0.0000
ATOM 50 H 1 17.579 16.881 13.750 2.47 1.00
H 0.0000
ATOM 51 O 1 16.337 15.205 13.885 3.00 1.00
O 0.0000
ATOM 52 C 1 17.494 14.425 13.850 3.40 1.00
C 0.0000
ATOM 53 H 1 17.557 13.998 12.853 2.47 1.00
H 0.0000
ATOM 54 H 1 18.431 14.934 14.127 2.47 1.00
H 0.0000
ATOM 55 C 1 17.439 13.209 14.742 3.40 1.00
C 0.0000
ATOM 56 H 1 18.213 12.490 14.459 2.47 1.00
H 0.0000
ATOM 57 H 1 16.500 12.697 14.464 2.47 1.00
H 0.0000
ATOM 58 O 1 17.509 13.431 16.163 3.00 1.00
O 0.0000
ATOM 59 C 1 18.729 14.027 16.565 3.40 1.00
C 0.0000
ATOM 60 H 1 19.475 13.392 16.249 2.47 1.00
H 0.0000
ATOM 61 H 1 18.902 14.997 16.162 2.47 1.00
H 0.0000
ATOM 62 C 1 18.758 14.067 18.126 3.40 1.00
C 0.0000
ATOM 63 H 1 18.340 13.134 18.551 2.47 1.00
H 0.0000
ATOM 64 H 1 18.217 14.851 18.605 2.47 1.00
H 0.0000
ATOM 65 O 1 20.109 14.117 18.541 3.07 1.00
O 0.0000
ATOM 66 H 1 20.028 14.134 19.538 0.00 1.00
H 0.0000
thanks
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Received on Tue Jul 08 2014 - 11:30:02 PDT
