AMBER Archive (2008)

Subject: Re: AMBER: mol2, xleap, Segmentation fault

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Mon Aug 25 2008 - 09:38:28 CDT

Hi,
 
Looks like some carbons have five bonds in your molecule.

jenk

Cenk Andac, M.S., Ph.D. Candidate
School of Pharmacy at
Gazi University-Ankara Turkiye

Address: Bandirma Sok. No:6

Etiler, Ankara, 06330 Turkey

Cell: +90-(536)-4813012

E-Mail:cenk_andac_at_yahoo.com

--- On Mon, 8/25/08, Anna Karawajczyk <a.karawajczyk_at_cmbi.ru.nl> wrote:

From: Anna Karawajczyk <a.karawajczyk_at_cmbi.ru.nl>
Subject: AMBER: mol2, xleap, Segmentation fault
To: amber_at_scripps.edu
Date: Monday, August 25, 2008, 8:01 AM

Dear AMBER users,

I am using amber8 and lately I was trying to load attached mol2 file
into xleap.
I have used following commend:
bcl=loadmol2 bcl.mol2
and xleap crushes immediately.
The only message I see is: Segmentation fault.
Do you know what is wrong and how to solve it?

Greetings,
Anna

@<TRIPOS>MOLECULE
BCL
  140 144 1 0 0
SMALL
bcc

@<TRIPOS>ATOM
      1 MG 13.6280 95.2510 30.8500 MG 853 BCL 0.134000
      2 CHA 16.1560 97.1550 29.4050 CD 853 BCL 0.065000
      3 CHB 12.3070 94.6030 27.8640 CD 853 BCL -0.224000
      4 HHB 11.9150 94.4370 26.9590 HA 853 BCL 0.115000
      5 CHC 11.3230 93.3430 32.3370 CD 853 BCL -0.273000
      6 HHC 10.6490 92.7770 32.8120 HA 853 BCL 0.168000
      7 CHD 15.0500 95.8930 33.9240 CD 853 BCL -0.262000
      8 HHD 15.4620 96.0880 34.8140 HA 853 BCL 0.147000
      9 NA 14.1530 95.8110 28.9620 NS 853 BCL 0.036000
     10 C1A 15.2300 96.5990 28.5160 CM 853 BCL -0.119000
     11 C2A 15.2040 96.6740 27.0380 CT 853 BCL -0.037000
     12 H2A 15.2480 97.5530 26.5630 HC 853 BCL 0.091000
     13 C3A 14.0010 95.9540 26.6270 CT 853 BCL 0.008000
     14 H3A 14.2070 95.2110 25.9900 HC 853 BCL 0.262000
     15 C4A 13.4150 95.4090 27.8590 CM 853 BCL -0.016000
     16 CMA 13.0470 96.9940 26.0260 CT 853 BCL -0.275000
     17 HMA1 12.1960 96.5660 25.7210 HC 853 BCL 0.070000
     18 HMA2 13.4620 97.4480 25.2380 HC 853 BCL 0.070000
     19 HMA3 12.8140 97.6970 26.6980 HC 853 BCL 0.070000
     20 CAA 16.2850 95.5320 27.0180 CT 853 BCL -0.063000
     21 HAA1 15.9380 94.7600 27.5500 HC 853 BCL 0.038202
     22 HAA2 17.1200 95.8810 27.4430 HC 853 BCL 0.038002
     23 CBA 16.7470 94.9260 25.7840 CT 853 BCL -0.231000
     24 HBA1 15.9560 94.8540 25.1760 HC 853 BCL 0.083020
     25 HBA2 17.4200 95.5470 25.3840 HC 853 BCL 0.083020
     26 CGA 17.3740 93.5470 25.9690 C 853 BCL 0.661000
     27 O1A 18.4350 93.3320 25.4060 O 853 BCL -0.521000
     28 O2A 16.8100 92.6280 26.6650 OS 853 BCL -0.325000
     29 NB 12.0060 94.1040 30.1880 NB 853 BCL -0.055000
     30 C1B 11.6360 93.9790 28.8960 CC 853 BCL -0.027000
     31 C2B 10.5120 93.1300 28.7550 C* 853 BCL 0.198000
     32 C3B 10.1470 92.6640 30.1000 C* 853 BCL 0.199000
     33 C4B 11.1340 93.3520 30.9300 CC 853 BCL -0.418000
     34 CMB 9.9450 92.8580 27.3140 CT 853 BCL -0.238000
     35 HMB1 9.1550 92.2460 27.3490 HC 853 BCL 0.081330
     36 HMB2 10.6370 92.4330 26.7310 HC 853 BCL 0.081330
     37 HMB3 9.6550 93.7090 26.8760 HC 853 BCL 0.081330
     38 CAB 9.0340 91.7070 30.5690 C 853 BCL 0.695000
     39 OBB 8.9460 91.4410 31.7860 O 853 BCL -0.537000
     40 CBB 8.0720 91.0850 29.5240 CT 853 BCL -0.392000
     41 HBB1 7.4030 90.4870 29.9650 HC 853 BCL 0.103330
     42 HBB2 8.5750 90.5410 28.8530 HC 853 BCL 0.103330
     43 HBB3 7.5710 91.7960 29.0300 HC 853 BCL 0.103330
     44 NC 13.2350 94.7280 32.7830 NS 853 BCL 0.072000
     45 C1C 12.2080 93.9260 33.1880 CM 853 BCL -0.088000
     46 C2C 12.1720 93.7420 34.6820 CT 853 BCL 0.308000
     47 H2C 12.2200 92.7840 34.9650 HC 853 BCL -0.014000
     48 C3C 13.3670 94.5220 35.1460 CT 853 BCL 0.068000
     49 H3C 13.1550 95.2530 35.7950 HC 853 BCL 0.015000
     50 C4C 13.9400 95.1010 33.9160 CM 853 BCL -0.063000
     51 CMC 10.8650 94.3090 35.2590 CT 853 BCL -0.301000
     52 HMC1 10.8310 94.1920 36.2520 HC 853 BCL 0.072330
     53 HMC2 10.0700 93.8460 34.8670 HC 853 BCL 0.072330
     54 HMC3 10.7800 95.2860 35.0620 HC 853 BCL 0.072330
     55 CAC 14.3550 93.4600 35.7180 CT 853 BCL 0.064000
     56 HAC1 13.9580 93.0790 36.5530 HC 853 BCL 0.005000
     57 HAC2 15.2160 93.9180 35.9370 HC 853 BCL 0.005000
     58 CBC 14.6710 92.2860 34.7630 CT 853 BCL -0.251000
     59 HBC1 15.3080 91.6410 35.1860 HC 853 BCL 0.057660
     60 HBC2 15.0860 92.6160 33.9150 HC 853 BCL 0.057660
     61 HBC3 13.8390 91.7850 34.5240 HC 853 BCL 0.057660
     62 ND 15.2310 96.2940 31.5340 NB 853 BCL 0.065000
     63 C1D 15.6540 96.4470 32.8240 CC 853 BCL -0.050000
     64 C2D 16.8010 97.2550 32.8880 C* 853 BCL 0.227000
     65 C3D 17.1630 97.6490 31.4920 C* 853 BCL -0.239000
     66 C4D 16.1320 97.0020 30.7760 CC 853 BCL -0.131000
     67 CMD 17.6190 97.7050 34.1310 CT 853 BCL -0.307000
     68 HMD1 18.3910 98.2810 33.8630 HC 853 BCL 0.096330
     69 HMD2 17.9820 96.9160 34.6260 HC 853 BCL 0.096330
     70 HMD3 17.0490 98.2290 34.7640 HC 853 BCL 0.096330
     71 CAD 17.9490 98.3070 30.5080 C 853 BCL 0.542000
     72 OBD 18.9530 98.9830 30.8210 O 853 BCL -0.510000
     73 CBD 17.3860 98.0310 29.1130 CT 853 BCL -0.202000
     74 HBD 17.9660 97.5350 28.4670 HC 853 BCL 0.071000
     75 CGD 17.1440 99.4080 28.4370 C 853 BCL 0.735000
     76 O1D 18.0310 99.9130 27.7510 O 853 BCL -0.539000
     77 O2D 15.9890 99.9370 28.6360 OS 853 BCL -0.489000
     78 CED 15.5560 101.2010 28.0940 CT 853 BCL 0.015000
     79 HED1 14.6210 101.4120 28.3800 H1 853 BCL 0.066330
     80 HED2 15.5760 101.1880 27.0940 H1 853 BCL 0.066330
     81 HED3 16.1480 101.9450 28.4030 H1 853 BCL 0.066330
     82 C1 17.5100 91.3040 26.7150 CT 853 BCL 0.392990
     83 H11 17.3390 90.8430 27.5860 H1 853 BCL 0.006500
     84 H12 18.4950 91.4170 26.5850 H1 853 BCL 0.006500
     85 C2 16.9200 90.5320 25.5900 CM 853 BCL -0.342000
     86 H2 16.0160 90.1360 25.7530 HA 853 BCL 0.133000
     87 C3 17.4920 90.2880 24.3020 CM 853 BCL 0.055000
     88 C4 18.8640 90.7700 23.8390 CT 853 BCL -0.301000
     89 H41 19.0480 90.4790 22.9000 HC 853 BCL 0.092666
     90 H42 19.5880 90.4030 24.4230 HC 853 BCL 0.092666
     91 H43 18.9220 91.7680 23.8680 HC 853 BCL 0.092666
     92 C5 16.7030 89.5190 23.2600 CT 853 BCL 0.098000
     93 H51 17.3350 88.8940 22.8010 HC 853 BCL 0.007500
     94 H52 16.0010 88.9920 23.7390 HC 853 BCL 0.007500
     95 C6 16.0050 90.2570 22.1910 CT 853 BCL -0.180000
     96 H61 16.6160 90.9670 21.8410 HC 853 BCL 0.090000
     97 H62 15.7800 89.6180 21.4560 HC 853 BCL 0.090000
     98 C7 14.7280 90.8890 22.7520 CT 853 BCL -0.180000
     99 H71 13.9640 90.2880 22.5180 HC 853 BCL 0.090000
    100 H72 14.8230 90.9350 23.7460 HC 853 BCL 0.090000
    101 C8 14.3990 92.3070 22.2360 CT 853 BCL -0.090000
    102 H8 14.3110 92.2300 21.2430 HC 853 BCL 0.090000
    103 C9 15.5030 93.3320 22.4970 CT 853 BCL -0.270000
    104 H91 15.2460 94.2330 22.1470 HC 853 BCL 0.090000
    105 H92 16.3560 93.0610 22.0520 HC 853 BCL 0.090000
    106 H93 15.6830 93.4230 23.4760 HC 853 BCL 0.090000
    107 C10 13.0910 92.8090 22.8720 CT 853 BCL -0.180000
    108 H101 13.2440 92.9370 23.8520 HC 853 BCL 0.090000
    109 H102 12.3850 92.1150 22.7330 HC 853 BCL 0.090000
    110 C11 12.5590 94.1060 22.3280 CT 853 BCL -0.180000
    111 H111 13.2220 94.8330 22.5030 HC 853 BCL 0.090000
    112 H112 12.4150 94.0160 21.3430 HC 853 BCL 0.090000
    113 C12 11.2470 94.4470 23.0000 CT 853 BCL -0.180000
    114 H121 10.6170 93.6890 22.8320 HC 853 BCL 0.090000
    115 H122 11.4220 94.5240 23.9810 HC 853 BCL 0.090000
    116 C13 10.5840 95.7580 22.5120 CT 853 BCL -0.090000
    117 H13 10.4270 95.7510 21.5240 HC 853 BCL 0.090000
    118 C14 11.4610 97.0080 22.7220 CT 853 BCL -0.270000
    119 H141 10.9970 97.8310 22.3940 HC 853 BCL 0.090000
    120 H142 12.3260 96.9260 22.2280 HC 853 BCL 0.090000
    121 H143 11.6720 97.1390 23.6910 HC 853 BCL 0.090000
    122 C15 9.2760 95.8290 23.2710 CT 853 BCL -0.180000
    123 H151 9.3770 95.3470 24.1410 HC 853 BCL 0.090000
    124 H152 9.0510 96.7880 23.4450 HC 853 BCL 0.090000
    125 C16 8.1530 95.1910 22.4770 CT 853 BCL -0.180000
    126 H161 8.0710 95.6560 21.5960 HC 853 BCL 0.090000
    127 H162 8.3670 94.2260 22.3260 HC 853 BCL 0.090000
    128 C17 6.8360 95.2890 23.2030 CT 853 BCL -0.180000
    129 H171 6.6970 94.4370 23.7080 HC 853 BCL 0.090000
    130 H172 6.8940 96.0520 23.8460 HC 853 BCL 0.090000
    131 C18 5.6360 95.5150 22.2680 CT 853 BCL -0.090000
    132 H18 5.7790 96.3570 21.7480 HC 853 BCL 0.090000
    133 C19 4.3810 95.6320 23.1070 CT 853 BCL -0.270000
    134 H191 3.5770 95.7800 22.5310 HC 853 BCL 0.090000
    135 H192 4.4470 96.3990 23.7450 HC 853 BCL 0.090000
    136 H193 4.2280 94.8000 23.6400 HC 853 BCL 0.090000
    137 C20 5.4720 94.3390 21.2880 CT 853 BCL -0.270000
    138 H201 4.6920 94.4850 20.6800 HC 853 BCL 0.090000
    139 H202 5.3220 93.4810 21.7800 HC 853 BCL 0.090000
    140 H203 6.2880 94.2290 20.7200 HC 853 BCL 0.090000
@<TRIPOS>BOND
     1 2 10 1
     2 2 66 2
     3 2 73 1
     4 3 4 1
     5 3 15 2
     6 3 30 1
     7 5 6 1
     8 5 33 2
     9 5 45 1
    10 7 8 1
    11 7 50 2
    12 7 63 1
    13 9 10 2
    14 9 15 1
    15 10 11 1
    16 11 12 1
    17 11 13 1
    18 11 20 1
    19 13 14 1
    20 13 15 1
    21 13 16 1
    22 16 17 1
    23 16 18 1
    24 16 19 1
    25 20 21 1
    26 20 22 1
    27 20 23 1
    28 23 24 1
    29 23 25 1
    30 23 26 1
    31 26 27 2
    32 26 28 1
    33 28 82 1
    34 29 30 2
    35 29 33 1
    36 30 31 1
    37 31 32 2
    38 31 34 1
    39 32 33 1
    40 32 38 1
    41 34 35 1
    42 34 36 1
    43 34 37 1
    44 38 39 2
    45 38 40 1
    46 40 41 1
    47 40 42 1
    48 40 43 1
    49 44 45 2
    50 44 50 1
    51 45 46 1
    52 46 47 1
    53 46 48 1
    54 46 51 1
    55 48 49 1
    56 48 50 1
    57 48 55 1
    58 51 52 1
    59 51 53 1
    60 51 54 1
    61 55 56 1
    62 55 57 1
    63 55 58 1
    64 58 59 1
    65 58 60 1
    66 58 61 1
    67 62 63 ar
    68 62 66 ar
    69 63 64 ar
    70 64 65 ar
    71 64 67 1
    72 65 66 ar
    73 65 71 1
    74 67 68 1
    75 67 69 1
    76 67 70 1
    77 71 72 2
    78 71 73 1
    79 73 74 1
    80 73 75 1
    81 75 76 2
    82 75 77 1
    83 77 78 1
    84 78 79 1
    85 78 80 1
    86 78 81 1
    87 82 83 1
    88 82 84 1
    89 82 85 1
    90 85 86 1
    91 85 87 2
    92 87 88 1
    93 87 92 1
    94 88 89 1
    95 88 90 1
    96 88 91 1
    97 92 93 1
    98 92 94 1
    99 92 95 1
   100 95 96 1
   101 95 97 1
   102 95 98 1
   103 98 99 1
   104 98 100 1
   105 98 101 1
   106 101 102 1
   107 101 103 1
   108 101 107 1
   109 103 104 1
   110 103 105 1
   111 103 106 1
   112 107 108 1
   113 107 109 1
   114 107 110 1
   115 110 111 1
   116 110 112 1
   117 110 113 1
   118 113 114 1
   119 113 115 1
   120 113 116 1
   121 116 117 1
   122 116 118 1
   123 116 122 1
   124 118 119 1
   125 118 120 1
   126 118 121 1
   127 122 123 1
   128 122 124 1
   129 122 125 1
   130 125 126 1
   131 125 127 1
   132 125 128 1
   133 128 129 1
   134 128 130 1
   135 128 131 1
   136 131 132 1
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   139 133 134 1
   140 133 135 1
   141 133 136 1
   142 137 138 1
   143 137 139 1
   144 137 140 1
@<TRIPOS>SUBSTRUCTURE
     1 BCL 1 TEMP 0 **** **** 0 ROOT

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