[AMBER] antechamber am1bcc stops with no error message from Danny Xu on 2011-09-05 (Amber Archive Sep 2011)

From: Danny Xu <quantum_mania.yahoo.com>
Date: Mon, 5 Sep 2011 21:37:38 -0700 (PDT)

Hi, I tried to assign am1bcc charge to the attached mol2 file using antechamber. Sqm calculation finished just fine (sqm.out is also attached). However, antechamber failed to create ANTECHAMBER_AM1BCC_PRE.AC file and no error was printed out. The molecule has 156 atoms, below MAXATOM=256 defined for antechamber. I'd really appreciate if anyone can help pin down the problem. DX mol2 file: ================================================ .<TRIPOS>MOLECULE title: molecule 1 156 155 5 SMALL USER_CHARGES .<TRIPOS>ATOM 1 N1 -2.7615 0.3975 -0.4243 N.3 1 PEG 0.0000 2 C1 -1.5566 1.2038 -0.4225 C.3 1 PEG 0.0000 3 C2 -0.3282 0.3008 -0.2574 C.3 1 PEG 0.0000 4 C3 0.9730 1.1152 -0.1538 C.3 1 PEG 0.0000 5 C4 2.2671 0.2752 -0.1166 C.3 1 PEG 0.0000 6 H1 -3.5762 0.9927 -0.5059 H 1 PEG 0.0000 7 H2 -2.7787 -0.2162 -1.2264 H 1 PEG 0.0000 8 H3 -1.4923 1.7763 -1.3503 H 1 PEG 0.0000 9 H4 -1.6108 1.9161 0.4019 H 1 PEG 0.0000 10 H5 -0.4563 -0.3191 0.6329 H 1 PEG 0.0000 11 H6 -0.2577 -0.3834 -1.1046 H 1 PEG 0.0000 12 H7 1.0209 1.7771 -1.0195 H 1 PEG 0.0000 13 H8 0.9316 1.7685 0.7200 H 1 PEG 0.0000 14 C5 3.4904 1.2150 -0.2117 C.3 1 PEG 0.0000 15 C6 2.3333 -0.6222 1.1435 C.3 1 PEG 0.0000 16 H9 2.2612 -0.3681 -0.9989 H 1 PEG 0.0000 17 O1 4.6386 0.4735 -0.5588 O.3 1 PEG 0.0000 18 H10 3.3440 1.9869 -0.9665 H 1 PEG 0.0000 19 H11 3.6582 1.7245 0.7383 H 1 PEG 0.0000 20 O2 3.4924 -1.4395 1.1290 O.3 1 PEG 0.0000 21 H12 2.3273 -0.0166 2.0514 H 1 PEG 0.0000 22 H13 1.4658 -1.2824 1.1978 H 1 PEG 0.0000 23 C1 3.5181 -2.2404 2.2892 C.3 1 PEG 0.0000 24 C2 4.7683 -3.1219 2.2736 C.3 1 PEG 0.0000 25 O1 4.7811 -3.9174 3.4393 O.3 1 PEG 0.0000 26 H2 2.6289 -2.8704 2.3148 H 1 PEG 0.0000 27 H3 3.5349 -1.6006 3.1715 H 1 PEG 0.0000 28 H4 4.7514 -3.7618 1.3913 H 1 PEG 0.0000 29 H5 5.6574 -2.4919 2.2479 H 1 PEG 0.0000 30 C1 5.9292 -4.7358 3.4381 C.3 1 PEG 0.0000 31 C2 5.9431 -5.5982 4.7017 C.3 1 PEG 0.0000 32 O1 7.0964 -6.4114 4.6874 O.3 1 PEG 0.0000 33 H2 6.8211 -4.1096 3.4152 H 1 PEG 0.0000 34 H3 5.9151 -5.3795 2.5585 H 1 PEG 0.0000 35 H4 5.9572 -4.9545 5.5813 H 1 PEG 0.0000 36 H5 5.0512 -6.2244 4.7247 H 1 PEG 0.0000 37 C1 7.1221 -7.2123 5.8475 C.3 1 PEG 0.0000 38 C2 8.3724 -8.0939 5.8319 C.3 1 PEG 0.0000 39 O1 8.3851 -8.8894 6.9976 O.3 1 PEG 0.0000 40 H2 6.2330 -7.8423 5.8732 H 1 PEG 0.0000 41 H3 7.1390 -6.5725 6.7298 H 1 PEG 0.0000 42 H4 8.3555 -8.7337 4.9496 H 1 PEG 0.0000 43 H5 9.2615 -7.4639 5.8062 H 1 PEG 0.0000 44 C1 9.5333 -9.7078 6.9964 C.3 1 PEG 0.0000 45 C2 9.5471 -10.5701 8.2601 C.3 1 PEG 0.0000 46 O1 10.7005 -11.3833 8.2457 O.3 1 PEG 0.0000 47 H2 10.4252 -9.0816 6.9735 H 1 PEG 0.0000 48 H3 9.5192 -10.3514 6.1168 H 1 PEG 0.0000 49 H4 9.5612 -9.9265 9.1396 H 1 PEG 0.0000 50 H5 8.6552 -11.1963 8.2830 H 1 PEG 0.0000 51 C1 10.7261 -12.1843 9.4058 C.3 1 PEG 0.0000 52 C2 11.9764 -13.0658 9.3902 C.3 1 PEG 0.0000 53 O1 11.9892 -13.8613 10.5559 O.3 1 PEG 0.0000 54 H2 9.8370 -12.8143 9.4315 H 1 PEG 0.0000 55 H3 10.7430 -11.5444 10.2881 H 1 PEG 0.0000 56 H4 11.9595 -13.7056 8.5079 H 1 PEG 0.0000 57 H5 12.8655 -12.4358 9.3646 H 1 PEG 0.0000 58 C1 13.1373 -14.6797 10.5547 C.3 1 PEG 0.0000 59 C2 13.1511 -15.5420 11.8184 C.3 1 PEG 0.0000 60 O1 14.3045 -16.3552 11.8040 O.3 1 PEG 0.0000 61 H2 14.0292 -14.0535 10.5318 H 1 PEG 0.0000 62 H3 13.1232 -15.3233 9.6752 H 1 PEG 0.0000 63 H4 13.1653 -14.8984 12.6979 H 1 PEG 0.0000 64 H5 12.2593 -16.1682 11.8413 H 1 PEG 0.0000 65 C1 14.3302 -17.1562 12.9641 C.3 1 PEG 0.0000 66 C2 15.5805 -18.0377 12.9485 C.3 1 PEG 0.0000 67 O1 15.5932 -18.8332 14.1142 O.3 1 PEG 0.0000 68 H2 13.4411 -17.7862 12.9898 H 1 PEG 0.0000 69 H3 14.3471 -16.5164 13.8464 H 1 PEG 0.0000 70 H4 15.5636 -18.6775 12.0662 H 1 PEG 0.0000 71 H5 16.4696 -17.4077 12.9229 H 1 PEG 0.0000 72 C1 16.7414 -19.6516 14.1130 C.3 1 PEG 0.0000 73 C2 16.7552 -20.5139 15.3767 C.3 1 PEG 0.0000 74 O1 17.9086 -21.3272 15.3623 O.3 1 PEG 0.0000 75 H2 17.6333 -19.0254 14.0901 H 1 PEG 0.0000 76 H3 16.7272 -20.2952 13.2335 H 1 PEG 0.0000 77 H4 16.7693 -19.8703 16.2563 H 1 PEG 0.0000 78 H5 15.8633 -21.1401 15.3996 H 1 PEG 0.0000 79 C1 17.9342 -22.1281 16.5224 C.3 1 PEG 0.0000 80 C2 19.1845 -23.0097 16.5069 C.3 1 PEG 0.0000 81 O1 19.1972 -23.8051 17.6726 O.3 1 PEG 0.0000 82 H2 17.0451 -22.7581 16.5481 H 1 PEG 0.0000 83 H3 17.9511 -21.4883 17.4047 H 1 PEG 0.0000 84 H4 19.1676 -23.6495 15.6245 H 1 PEG 0.0000 85 H5 20.0736 -22.3796 16.4812 H 1 PEG 0.0000 86 C86 20.3454 -24.6235 17.6714 C.3 1 PEG 0.0000 87 H87 20.3550 -25.2540 18.5957 H 1 PEG 0.0000 88 H88 20.3311 -25.2849 16.7690 H 1 PEG 0.0000 89 H89 21.2613 -23.9812 17.6485 H 1 PEG 0.0000 90 C1 5.7493 1.3380 -0.6433 C.3 1 PEG 0.0000 91 C2 6.9950 0.5337 -1.0200 C.3 1 PEG 0.0000 92 O1 8.0979 1.4106 -1.1009 O.3 1 PEG 0.0000 93 H2 5.9065 1.8221 0.3205 H 1 PEG 0.0000 94 H3 5.5620 2.0961 -1.4038 H 1 PEG 0.0000 95 H4 7.1823 -0.2244 -0.2595 H 1 PEG 0.0000 96 H5 6.8379 0.0496 -1.9838 H 1 PEG 0.0000 97 C1 9.2541 0.6819 -1.4477 C.3 1 PEG 0.0000 98 C2 10.4497 1.6325 -1.5354 C.3 1 PEG 0.0000 99 O1 11.5988 0.8905 -1.8829 O.3 1 PEG 0.0000 100 H2 9.1023 0.1981 -2.4126 H 1 PEG 0.0000 101 H3 9.4468 -0.0759 -0.6882 H 1 PEG 0.0000 102 H4 10.2570 2.3902 -2.2949 H 1 PEG 0.0000 103 H5 10.6015 2.1162 -0.5706 H 1 PEG 0.0000 104 C1 12.7095 1.7549 -1.9674 C.3 1 PEG 0.0000 105 C2 13.9552 0.9506 -2.3440 C.3 1 PEG 0.0000 106 O1 15.0581 1.8275 -2.4250 O.3 1 PEG 0.0000 107 H2 12.8666 2.2390 -1.0035 H 1 PEG 0.0000 108 H3 12.5222 2.5130 -2.7279 H 1 PEG 0.0000 109 H4 14.1425 0.1925 -1.5835 H 1 PEG 0.0000 110 H5 13.7981 0.4665 -3.3079 H 1 PEG 0.0000 111 C1 16.2143 1.0988 -2.7717 C.3 1 PEG 0.0000 112 C2 17.4098 2.0494 -2.8595 C.3 1 PEG 0.0000 113 O1 18.5590 1.3074 -3.2069 O.3 1 PEG 0.0000 114 H2 16.0625 0.6150 -3.7366 H 1 PEG 0.0000 115 H3 16.4069 0.3410 -2.0122 H 1 PEG 0.0000 116 H4 17.2172 2.8071 -3.6190 H 1 PEG 0.0000 117 H5 17.5616 2.5331 -1.8946 H 1 PEG 0.0000 118 C1 19.6697 2.1719 -3.2914 C.3 1 PEG 0.0000 119 C2 20.9154 1.3675 -3.6681 C.3 1 PEG 0.0000 120 O1 22.0182 2.2444 -3.7490 O.3 1 PEG 0.0000 121 H2 19.8268 2.6560 -2.3276 H 1 PEG 0.0000 122 H3 19.4824 2.9299 -4.0519 H 1 PEG 0.0000 123 H4 21.1027 0.6094 -2.9076 H 1 PEG 0.0000 124 H5 20.7582 0.8834 -4.6319 H 1 PEG 0.0000 125 C1 23.1745 1.5157 -4.0958 C.3 1 PEG 0.0000 126 C2 24.3700 2.4663 -4.1835 C.3 1 PEG 0.0000 127 O1 25.5191 1.7243 -4.5310 O.3 1 PEG 0.0000 128 H2 23.0227 1.0319 -5.0607 H 1 PEG 0.0000 129 H3 23.3671 0.7580 -3.3363 H 1 PEG 0.0000 130 H4 24.1773 3.2240 -4.9430 H 1 PEG 0.0000 131 H5 24.5218 2.9501 -3.2186 H 1 PEG 0.0000 132 C1 26.6298 2.5888 -4.6155 C.3 1 PEG 0.0000 133 C2 27.8755 1.7844 -4.9921 C.3 1 PEG 0.0000 134 O1 28.9784 2.6613 -5.0731 O.3 1 PEG 0.0000 135 H2 26.7870 3.0729 -3.6516 H 1 PEG 0.0000 136 H3 26.4425 3.3468 -5.3760 H 1 PEG 0.0000 137 H4 28.0628 1.0264 -4.2316 H 1 PEG 0.0000 138 H5 27.7184 1.3003 -5.9560 H 1 PEG 0.0000 139 C1 30.1346 1.9326 -5.4198 C.3 1 PEG 0.0000 140 C2 31.3301 2.8832 -5.5076 C.3 1 PEG 0.0000 141 O1 32.4793 2.1412 -5.8550 O.3 1 PEG 0.0000 142 H2 29.9828 1.4489 -6.3847 H 1 PEG 0.0000 143 H3 30.3273 1.1749 -4.6603 H 1 PEG 0.0000 144 H4 31.1375 3.6410 -6.2670 H 1 PEG 0.0000 145 H5 31.4819 3.3670 -4.5427 H 1 PEG 0.0000 146 C1 33.5900 3.0057 -5.9395 C.3 1 PEG 0.0000 147 C2 34.8357 2.2014 -6.3161 C.3 1 PEG 0.0000 148 O1 35.9385 3.0783 -6.3971 O.3 1 PEG 0.0000 149 H2 33.7471 3.4898 -4.9756 H 1 PEG 0.0000 150 H3 33.4027 3.7638 -6.7000 H 1 PEG 0.0000 151 H4 35.0230 1.4433 -5.5557 H 1 PEG 0.0000 152 H5 34.6785 1.7173 -7.2800 H 1 PEG 0.0000 153 C153 37.0948 2.3496 -6.7438 C.3 1 PEG 0.0000 154 H154 37.9688 3.0452 -6.8079 H 1 PEG 0.0000 155 H155 37.2933 1.5720 -5.9642 H 1 PEG 0.0000 156 H156 36.9397 1.8533 -7.7346 H 1 PEG 0.0000 .<TRIPOS>BOND 1 1 2 1 2 1 6 1 3 1 7 1 4 2 3 1 5 2 8 1 6 2 9 1 7 3 4 1 8 3 10 1 9 3 11 1 10 4 5 1 11 4 12 1 12 4 13 1 13 5 14 1 14 5 15 1 15 5 16 1 16 14 17 1 17 14 18 1 18 14 19 1 19 15 20 1 20 15 21 1 21 15 22 1 22 17 90 1 23 20 23 1 24 23 24 1 25 23 26 1 26 23 27 1 27 24 25 1 28 24 28 1 29 24 29 1 30 25 30 1 31 30 31 1 32 30 33 1 33 30 34 1 34 31 32 1 35 31 35 1 36 31 36 1 37 32 37 1 38 37 38 1 39 37 40 1 40 37 41 1 41 38 39 1 42 38 42 1 43 38 43 1 44 39 44 1 45 44 45 1 46 44 47 1 47 44 48 1 48 45 46 1 49 45 49 1 50 45 50 1 51 46 51 1 52 51 52 1 53 51 54 1 54 51 55 1 55 52 53 1 56 52 56 1 57 52 57 1 58 53 58 1 59 58 59 1 60 58 61 1 61 58 62 1 62 59 60 1 63 59 63 1 64 59 64 1 65 60 65 1 66 65 66 1 67 65 68 1 68 65 69 1 69 66 67 1 70 66 70 1 71 66 71 1 72 67 72 1 73 72 73 1 74 72 75 1 75 72 76 1 76 73 74 1 77 73 77 1 78 73 78 1 79 74 79 1 80 79 80 1 81 79 82 1 82 79 83 1 83 80 81 1 84 80 84 1 85 80 85 1 86 81 86 1 87 86 87 1 88 86 88 1 89 86 89 1 90 90 91 1 91 90 93 1 92 90 94 1 93 91 92 1 94 91 95 1 95 91 96 1 96 92 97 1 97 97 98 1 98 97 100 1 99 97 101 1 100 98 99 1 101 98 102 1 102 98 103 1 103 99 104 1 104 104 105 1 105 104 107 1 106 104 108 1 107 105 106 1 108 105 109 1 109 105 110 1 110 106 111 1 111 111 112 1 112 111 114 1 113 111 115 1 114 112 113 1 115 112 116 1 116 112 117 1 117 113 118 1 118 118 119 1 119 118 121 1 120 118 122 1 121 119 120 1 122 119 123 1 123 119 124 1 124 120 125 1 125 125 126 1 126 125 128 1 127 125 129 1 128 126 127 1 129 126 130 1 130 126 131 1 131 127 132 1 132 132 133 1 133 132 135 1 134 132 136 1 135 133 134 1 136 133 137 1 137 133 138 1 138 134 139 1 139 139 140 1 140 139 142 1 141 139 143 1 142 140 141 1 143 140 144 1 144 140 145 1 145 141 146 1 146 146 147 1 147 146 149 1 148 146 150 1 149 147 148 1 150 147 151 1 151 147 152 1 152 148 153 1 153 153 154 1 154 153 155 1 155 153 156 1 .<TRIPOS>SUBSTRUCTURE 1 PEG 1 GROUP 0 **** 0 ROOT ========================================================================

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application/octet-stream attachment: PEG9_numbered.mol2

application/octet-stream attachment: sqm.out

Received on Mon Sep 05 2011 - 22:00:03 PDT