Multiple Molecule-Systems with Mopac?
Dear Subscribers,
we are using MOPAC 5.0 (purchased with SYBYL 6.0). Recent we would compute
a multi-molecule-system (see the *.dat-file below, generated with SYBYL).
After some computation-time MOPAC stopped (during the computation for the
first reaction coordinate) and print in his output-file (see below):
THREE ATOMS BEING USED TO DEFINE THE
COORDINATES OF A FOURTH ATOM, WHOSE BOND-ANGLE IS
NOT ZERO OR 180 DEGREEES, ARE IN AN ALMOST STRAIGHT
LINE. THERE IS A HIGH PROBABILITY THAT THE
COORDINATES OF THE ATOM WILL BE INCORRECT.
and at the end:
ATOMS 65, 63, AND 54 ARE WITHIN 0.0059 ANGSTROMS OF A STRAIGHT LINE
The bond-angle between theese 3 atoms, which are not connected, is 0 degrees.
A second attempt, using cartesian coordinates, showed the same results.
Can anybody give us hints for the handling of such multi-molecule-systems
with MOAPC?
Thank You for Your help. With best regards,
H. Schinke
############## Input (DAT)-File for the run ##############################
PM3 T=360000 NOINTER CHARGE-1
aceto_rxn.dat
isopropylchlorid + NH2 in acetonitril
0006 0.0000 0 0.0000 0 0.0000 0 0000 0000 0000
0006 1.5500 1 0.0000 0 0.0000 0 0001 0000 0000
0006 1.5514 1 111.1064 1 0.0000 0 0002 0001 0000
0017 1.7710 1 109.5989 1 -121.0562 1 0002 0001 0003
0007 3.5578 -1 80.7763 1 93.7999 1 0002 0001 0003
0001 1.1011 1 110.5590 1 -60.5032 1 0001 0002 0003
0001 1.0989 1 109.9108 1 -179.0905 1 0001 0002 0003
0001 1.1028 1 110.4057 1 60.9707 1 0001 0002 0003
0001 1.1043 1 109.7158 1 120.9287 1 0002 0001 0003
0001 1.1033 1 109.8467 1 179.2252 1 0003 0002 0001
0001 1.1019 1 110.1398 1 58.7459 1 0003 0002 0001
0001 1.1015 1 110.2444 1 -60.5427 1 0003 0002 0001
0001 1.0822 1 74.1199 1 -87.4158 1 0005 0002 0001
0001 1.0820 1 126.5937 1 15.1313 1 0005 0002 0001
0006 4.7255 1 94.3647 1 128.2758 1 0005 0002 0001
0007 1.1581 1 150.8418 1 -91.2513 1 0015 0005 0002
0006 1.4591 1 29.0551 1 88.8644 1 0015 0005 0002
0001 1.1001 1 109.3496 1 85.7222 1 0017 0015 0005
0001 1.1004 1 109.2794 1 -34.0471 1 0017 0015 0005
0001 1.1008 1 109.6514 1 -154.1209 1 0017 0015 0005
0006 3.5996 1 153.6728 1 -96.5280 1 0014 0005 0002
0007 1.1578 1 13.9165 1 146.8929 1 0021 0014 0005
0006 1.4574 1 166.0703 1 -32.8884 1 0021 0014 0005
0001 1.0985 1 109.5225 1 -46.5050 1 0023 0021 0014
0001 1.0990 1 109.5135 1 -166.5502 1 0023 0021 0014
0001 1.0988 1 109.5336 1 73.3020 1 0023 0021 0014
0006 3.1821 1 135.8468 1 -33.5144 1 0026 0023 0021
0007 1.1575 1 58.8166 1 -86.8753 1 0027 0026 0023
0006 1.4569 1 121.2665 1 93.3518 1 0027 0026 0023
0001 1.0995 1 109.1838 1 157.7614 1 0029 0027 0026
0001 1.0990 1 109.1728 1 38.1084 1 0029 0027 0026
0001 1.1001 1 109.6732 1 -81.9072 1 0029 0027 0026
0006 3.0767 1 103.4743 1 -51.4763 1 0025 0023 0021
0007 1.1575 1 76.3789 1 166.4251 1 0033 0025 0023
0006 1.4574 1 103.6952 1 -13.7778 1 0033 0025 0023
0001 1.0987 1 109.0487 1 -147.5827 1 0035 0033 0025
0001 1.1000 1 109.7437 1 92.3169 1 0035 0033 0025
0001 1.0985 1 109.6728 1 -27.9951 1 0035 0033 0025
0006 3.4510 1 108.8603 1 -165.3810 1 0031 0029 0027
0007 1.1576 1 46.9670 1 131.3490 1 0039 0031 0029
0006 1.4572 1 132.9267 1 -48.6902 1 0039 0031 0029
0001 1.0997 1 109.3387 1 93.5222 1 0041 0039 0031
0001 1.0980 1 109.2758 1 -26.5337 1 0041 0039 0031
0001 1.0987 1 109.8151 1 -146.1868 1 0041 0039 0031
0006 2.9482 1 112.4182 1 -121.6753 1 0011 0003 0002
0007 1.1579 1 90.4906 1 91.2241 1 0045 0011 0003
0006 1.4577 1 89.4953 1 -88.6234 1 0045 0011 0003
0001 1.0995 1 109.7035 1 149.5640 1 0047 0045 0011
0001 1.0982 1 109.2759 1 29.6008 1 0047 0045 0011
0001 1.0990 1 109.6324 1 -90.1483 1 0047 0045 0011
0006 4.5317 1 139.9017 1 -69.9744 1 0012 0003 0002
0007 1.1573 1 145.3014 1 -130.1153 1 0051 0012 0003
0006 1.4565 1 34.8458 1 49.8356 1 0051 0012 0003
0001 1.0993 1 108.9200 1 -157.5288 1 0053 0051 0012
0001 1.0994 1 110.0562 1 82.4921 1 0053 0051 0012
0001 1.0994 1 109.1379 1 -37.6058 1 0053 0051 0012
0006 3.4721 1 116.7486 1 -176.4873 1 0004 0002 0001
0007 1.1572 1 101.7777 1 86.5285 1 0057 0004 0002
0006 1.4560 1 78.1876 1 -93.6430 1 0057 0004 0002
0001 1.0984 1 109.8789 1 69.2024 1 0059 0057 0004
0001 1.0962 1 108.6552 1 -50.4940 1 0059 0057 0004
0001 1.0984 1 109.8177 1 -170.0241 1 0059 0057 0004
0006 4.4310 1 131.3391 1 -95.8235 1 0054 0053 0051
0007 1.1574 1 168.8801 1 -42.8294 1 0063 0054 0053
0006 1.4566 1 11.3006 1 137.2662 1 0063 0054 0053
0001 1.0997 1 109.2702 1 48.5555 1 0065 0063 0054
0001 1.0992 1 109.5672 1 -71.5576 1 0065 0063 0054
0001 1.0995 1 109.3136 1 168.5094 1 0065 0063 0054
0006 2.8666 1 111.9127 1 114.2402 1 0011 0003 0002
0007 1.1577 1 78.8063 1 126.9038 1 0069 0011 0003
0006 1.4573 1 101.1095 1 -52.9852 1 0069 0011 0003
0001 1.0988 1 109.4665 1 88.1980 1 0071 0069 0011
0001 1.0994 1 109.6016 1 -31.7086 1 0071 0069 0011
0001 1.0989 1 109.3863 1 -151.8561 1 0071 0069 0011
0006 3.1681 1 116.9983 1 65.3880 1 0014 0005 0002
0007 1.1577 1 68.7614 1 18.5956 1 0075 0014 0005
0006 1.4574 1 111.3471 1 -161.5537 1 0075 0014 0005
0001 1.0990 1 110.0250 1 -38.6061 1 0077 0075 0014
0001 1.0988 1 108.9522 1 -158.6613 1 0077 0075 0014
0001 1.0981 1 109.5142 1 81.4778 1 0077 0075 0014
0006 3.0430 1 101.6525 1 178.7693 1 0042 0041 0039
0007 1.1573 1 86.4724 1 -12.0939 1 0081 0042 0041
0006 1.4566 1 93.4012 1 167.6526 1 0081 0042 0041
0001 1.0988 1 110.0533 1 132.2910 1 0083 0081 0042
0001 1.0996 1 109.5192 1 11.8415 1 0083 0081 0042
0001 1.0989 1 108.6354 1 -107.8211 1 0083 0081 0042
0006 2.8961 1 117.9918 1 39.7798 1 0055 0053 0051
0007 1.1572 1 94.4558 1 -21.5512 1 0087 0055 0053
0006 1.4568 1 85.5489 1 158.3391 1 0087 0055 0053
0001 1.0993 1 109.4929 1 75.9636 1 0089 0087 0055
0001 1.0997 1 109.8437 1 -44.3760 1 0089 0087 0055
0001 1.0980 1 108.9221 1 -164.2069 1 0089 0087 0055
4.0 3.8 3.6 3.4 3.2 3.0 2.9 2.8 2.7 2.6 2.5 2.4 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6
1.5
####### end dat-file ########### start out-file ######################
---------------- stuff deleted ---------------------------------
RESTART FILE WRITTEN, TIME LEFT: 336271.4 GRAD.: 70.180 HEAT: 250.6730
CYCLE: 17 TIME:1985.31 TIME LEFT: 334286.1 GRAD.: 86.913 HEAT: 248.3024
CYCLE: 18 TIME: 318.24 TIME LEFT: 333967.8 GRAD.: 88.962 HEAT: 248.1202
RESTART FILE WRITTEN, TIME LEFT: 330634.8 GRAD.: 112.826 HEAT: 244.9363
CALCULATION ABANDONED AT THIS POINT
THREE ATOMS BEING USED TO DEFINE THE
COORDINATES OF A FOURTH ATOM, WHOSE BOND-ANGLE IS
NOT ZERO OR 180 DEGREEES, ARE IN AN ALMOST STRAIGHT
LINE. THERE IS A HIGH PROBABILITY THAT THE
COORDINATES OF THE ATOM WILL BE INCORRECT.
THE FAULTY ATOM IS ATOM NUMBER 66
---------------- stuff deleted ----------------------------------
53 C 1.43856 * 27.56940 * 47.24132 * 51 12 3
54 H 1.10289 * 113.07091 * -159.36420 * 53 51 12
55 H 1.10628 * 110.38282 * 82.03550 * 53 51 12
56 H 1.10154 * 110.86405 * -39.47341 * 53 51 12
57 C 4.08353 * 95.06319 * -183.15715 * 4 2 1
58 N 1.15994 * 115.38586 * 98.17581 * 57 4 2
59 C 1.43955 * 64.12061 * -80.79930 * 57 4 2
60 H 1.10829 * 109.67685 * 69.63226 * 59 57 4
61 H 1.10079 * 110.64538 * -49.08832 * 59 57 4
62 H 1.09725 * 110.82013 * -170.03940 * 59 57 4
63 C 4.37425 * 137.62500 * -102.46271 * 54 53 51
64 N 1.16069 * 185.63463 * -39.66892 * 63 54 53
65 C 1.44209 * 0.07684 * 131.59166 * 63 54 53
66 H 1.10339 * 111.26819 * 49.01765 * 65 63 54
---------------- stuff deleted ----------------------------------
ATOMS 65, 63, AND 54 ARE WITHIN 0.0059 ANGSTROMS OF A STRAIGHT LINE
################### end out-file #################################
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
=-= Heiko Schinke =-=
=-= Martin-Luther-University, Dept. of Biochemistry/Biotechnology =-=
=-= P. O. Box 8, D-4020 Halle/Saale, Germany =-=
=-= =-=
=-= Phone: ++49/345/617242 FAX: ++49/345/647161 =-=
=-= =-=
=-= E-Mail: schinke # - at - # biochemtech.uni-halle.dbp.de
=-=
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