AMBER Archive (2008)

Subject: 回复： RE: AMBER: A problem to loadup the molecular in the xleap

From: 捞毛 渔 (yulaomao1983_at_yahoo.com.cn)
Date: Sat Jan 19 2008 - 10:31:05 CST

Dear Dr Yong,
   
  The errors were just as I had not loaded up the imichange.prepin and imichange.frcmod. It said that some bond type and atom types could not be found.
  Tonight I ran the program again, but I still could not save the file. May be loading up the file in the format of mol2 was not the same as loading up the pdb file? I did all the thing as the tutorial.
   
  Another problem, when I saved the protein file (the receptor) as mol2 in sybyl. Then i loaded it up in the xleap, and displayed it. Unfortunately, some bonds of this receptor were also changed! So the receptor could not be saved in xleap to get the prmtop and inpcrd files also!
   
  I had attached these files to the email. I really hope you can provide me some help.
   
  Best wishes
   
  Rilei Yu
   
   
   

       
---------------------------------
雅虎邮箱传递新年祝福，个性贺卡送亲朋！

remark goes here
MASS

BOND
c -h4 348.60 1.084 same as c2-h4

ANGLE
c3-c -h4 43.800 127.530 same as c3-c2-h4
h4-c -o 55.400 120.000 same as hc-c -o

DIHE
c3-cc-ca-ca 1 2.550 180.000 2.000 same as X -c2-ca-X
cd-cc-ca-ca 1 2.550 180.000 2.000 same as X -c2-ca-X

IMPROPER
nh-nh-c2-nh 1.1 180.0 2.0 Using default value
c3-h4-c -o 10.5 180.0 2.0 General improper torsional angle (2 general atom types)
c3-n -c -o 10.5 180.0 2.0 General improper torsional angle (2 general atom types)
c3-ca-cc-cd 1.1 180.0 2.0 Using default value
cc-h4-cd-na 1.1 180.0 2.0 Using default value
ca-cd-na-hn 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
ca-ca-ca-na 1.1 180.0 2.0 Using default value
ca-ca-ca-cc 1.1 180.0 2.0 Using default value
ca-ca-ca-ha 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
c3-o -c -o 1.1 180.0 2.0 General improper torsional angle (1 general atom type)

NONBON


# Name: UNNAMED
# Creating user name: pub123
# Creation time: Thu Jan 17 16:12:17 2008

# Modifying user name: pub123
# Modification time: Thu Jan 17 17:14:55 2008

@<TRIPOS>MOLECULE
UNNAMED
  159 162 1 0 1
BIOPOLYMER
NO_CHARGES

@<TRIPOS>DICT
BIOPOLYMER macromol
@<TRIPOS>ATOM
      1 H1 -37.5788 -11.8425 -4.2750 H 1 M_1 0.0000
      2 H2 -38.0307 -13.4019 -4.8783 H 1 M_1 0.0000
      3 H3 -35.2753 -12.7934 -4.5337 H 1 M_1 0.0000
      4 H4 -35.8361 -12.0386 -6.0643 H 1 M_1 0.0000
      5 H5 -36.7269 -15.2655 -4.5155 H 1 M_1 0.0000
      6 H6 -35.8088 -16.8567 -6.6351 H 1 M_1 0.0000
      7 H7 -33.5333 -15.7075 -4.9813 H 1 M_1 0.0000
      8 H8 -33.7373 -15.7333 -6.7658 H 1 M_1 0.0000
      9 H9 -32.1194 -17.8815 -8.5888 H 1 M_1 0.0000
     10 H10 -30.3300 -18.0322 -8.6321 H 1 M_1 0.0000
     11 H11 -31.7446 -15.3232 -8.3943 H 1 M_1 0.0000
     12 H12 -30.8968 -16.0804 -11.0810 H 1 M_1 0.0000
     13 H13 -32.6837 -17.0510 -12.4585 H 1 M_1 0.0000
     14 H14 -35.4886 -17.1819 -12.1227 H 1 M_1 0.0000
     15 H15 -35.2922 -20.2320 -10.0734 H 1 M_1 0.0000
     16 H16 -34.9952 -21.1947 -12.2655 H 1 M_1 0.0000
     17 H17 -35.5115 -19.6892 -13.0984 H 1 M_1 0.0000
     18 H18 -37.2699 -21.7078 -11.5527 H 1 M_1 0.0000
     19 H19 -37.5026 -21.0901 -13.2233 H 1 M_1 0.0000
     20 H20 -38.8489 -19.9165 -11.1359 H 1 M_1 0.0000
     21 H21 -38.1688 -18.8887 -12.4428 H 1 M_1 0.0000
     22 H22 -39.3405 -18.2632 -10.0100 H 1 M_1 0.0000
     23 H23 -39.2809 -18.3189 -7.1813 H 1 M_1 0.0000
     24 H24 -38.7452 -21.8966 -6.7993 H 1 M_1 0.0000
     25 H25 -37.2764 -20.0977 -5.9135 H 1 M_1 0.0000
     26 H26 -36.9564 -19.4858 -3.3391 H 1 M_1 0.0000
     27 H27 -37.8091 -17.3553 -5.2610 H 1 M_1 0.0000
     28 H28 -39.2464 -17.4641 -2.9535 H 1 M_1 0.0000
     29 H29 -37.7200 -17.5241 -2.0084 H 1 M_1 0.0000
     30 H30 -39.6621 -18.8591 -0.6636 H 1 M_1 0.0000
     31 H31 -40.8231 -21.4642 -5.5219 H 1 M_1 0.0000
     32 H32 -41.1047 -21.4779 -7.2960 H 1 M_1 0.0000
     33 H33 -42.1580 -19.6957 -6.2332 H 1 M_1 0.0000
     34 H34 -38.1756 -16.1698 -8.0905 H 1 M_1 0.0000
     35 H35 -39.9034 -16.3194 -8.5583 H 1 M_1 0.0000
     36 H36 -34.1775 -15.5450 -13.7014 H 1 M_1 0.0000
     37 H37 -32.8383 -14.6728 -12.8816 H 1 M_1 0.0000
     38 H38 -34.5624 -13.2287 -12.3990 H 1 M_1 0.0000
     39 H39 -34.7106 -14.3281 -10.9862 H 1 M_1 0.0000
     40 H40 -36.9465 -13.8037 -11.9569 H 1 M_1 0.0000
     41 H41 -36.5685 -15.5507 -12.1349 H 1 M_1 0.0000
     42 H42 -35.7535 -13.8539 -14.4098 H 1 M_1 0.0000
     43 H43 -39.0371 -16.1701 -14.4733 H 1 M_1 0.0000
     44 H44 -38.2256 -15.8288 -12.9216 H 1 M_1 0.0000
     45 H45 -36.8377 -14.3189 -16.3887 H 1 M_1 0.0000
     46 H46 -38.2928 -15.3500 -16.3421 H 1 M_1 0.0000
     47 H47 -30.1661 -13.5135 -8.5788 H 1 M_1 0.0000
     48 H48 -28.0749 -12.7762 -7.8097 H 1 M_1 0.0000
     49 H49 -26.2017 -14.3934 -7.4659 H 1 M_1 0.0000
     50 H50 -27.2215 -15.7068 -8.1452 H 1 M_1 0.0000
     51 H51 -27.6965 -14.9036 -6.6104 H 1 M_1 0.0000
     52 H52 -28.5441 -14.7910 -10.6939 H 1 M_1 0.0000
     53 H53 -26.2732 -13.4158 -11.9421 H 1 M_1 0.0000
     54 H54 -27.8915 -15.3196 -13.5862 H 1 M_1 0.0000
     55 H55 -27.0283 -15.9991 -12.1650 H 1 M_1 0.0000
     56 H56 -26.3286 -14.3105 -15.5685 H 1 M_1 0.0000
     57 H57 -23.8913 -14.5903 -16.1241 H 1 M_1 0.0000
     58 H58 -24.6518 -16.2664 -11.0631 H 1 M_1 0.0000
     59 H59 -22.2190 -16.8526 -10.9098 H 1 M_1 0.0000
     60 H60 -20.7096 -16.4885 -12.8341 H 1 M_1 0.0000
     61 H61 -21.5745 -15.5210 -14.9764 H 1 M_1 0.0000
     62 H62 -26.5626 -12.3833 -14.2557 H 1 M_1 0.0000
     63 H63 -27.4786 -10.4119 -15.0941 H 1 M_1 0.0000
     64 H64 -29.6348 -9.5159 -14.2966 H 1 M_1 0.0000
     65 H65 -29.6743 -10.7307 -12.9740 H 1 M_1 0.0000
     66 H66 -30.1862 -12.4933 -14.4128 H 1 M_1 0.0000
     67 H67 -29.3441 -11.7413 -15.8100 H 1 M_1 0.0000
     68 H68 -31.2294 -10.1119 -16.0697 H 1 M_1 0.0000
     69 H69 -32.0715 -10.8632 -14.6722 H 1 M_1 0.0000
     70 H70 -31.3340 -12.8802 -16.5954 H 1 M_1 0.0000
     71 H71 -34.8220 -10.9546 -17.0656 H 1 M_1 0.0000
     72 H72 -33.5529 -10.2633 -16.0195 H 1 M_1 0.0000
     73 H73 -32.9846 -13.7524 -17.9538 H 1 M_1 0.0000
     74 H74 -34.5167 -12.8517 -18.1086 H 1 M_1 0.0000
     75 H75 -26.1603 -9.9060 -12.6936 H 1 M_1 0.0000
     76 N -37.3480 -12.6790 -4.7720 N.am 1 M_1 -0.3700
     77 CA -36.0235 -12.8437 -5.3385 C.3 1 M_1 0.0900
     78 C -35.9165 -14.1777 -6.0355 C.2 1 M_1 0.2000
     79 O -35.6485 -14.2137 -7.2265 O.2 1 M_1 -0.4000
     80 N -36.1125 -15.2893 -5.3041 N.am 1 M_1 -0.2600
     81 CA -35.4351 -16.5220 -5.6562 C.3 1 M_1 0.1400
     82 CB -33.9071 -16.2930 -5.8342 C.3 1 M_1 0.0400
     83 SG -32.9911 -17.8650 -5.9162 S.3 1 M_1 -0.0900
     84 SG -31.1171 -17.2960 -6.4642 S.3 1 M_1 -0.0900
     85 CB -31.1711 -17.4140 -8.2852 C.3 1 M_1 0.0400
     86 CA -31.0681 -16.0060 -8.9292 C.3 1 M_1 0.1400
     87 N -31.5421 -16.0910 -10.3172 N.am 1 M_1 -0.2600
     88 C -32.8731 -16.1840 -10.5352 C.2 1 M_1 0.2000
     89 CA -33.4541 -16.5030 -11.8962 C.3 1 M_1 0.1300
     90 N -34.5961 -17.4130 -11.7352 N.am 1 M_1 -0.2600
     91 C -34.4211 -18.5670 -11.0552 C.2 1 M_1 0.2000
     92 CA -35.5521 -19.5620 -10.9062 C.3 1 M_1 0.1300
     93 CB -35.6931 -20.3450 -12.2342 C.3 1 M_1 -0.0100
     94 CG -37.1561 -20.8340 -12.2112 C.3 1 M_1 -0.0300
     95 CD -37.9261 -19.6150 -11.6532 C.3 1 M_1 0.0400
     96 N -36.9271 -19.0910 -10.7212 N.am 1 M_1 -0.2500
     97 C -37.2301 -18.2850 -9.6622 C.2 1 M_1 0.2100
     98 CA -38.6521 -17.9800 -9.2002 C.3 1 M_1 0.1400
     99 N -38.9751 -18.7820 -8.0132 N.am 1 M_1 -0.2600
    100 C -38.8701 -20.1290 -8.0152 C.2 1 M_1 0.2100
    101 CA -39.1021 -20.8600 -6.7092 C.3 1 M_1 0.1500
    102 N -38.2521 -20.1910 -5.7152 N.am 1 M_1 -0.2600
    103 C -38.7181 -19.6940 -4.5452 C.2 1 M_1 0.2000
    104 CA -37.7591 -18.8470 -3.7362 C.3 1 M_1 0.1400
    105 N -37.2001 -17.8400 -4.6332 N.am 1 M_1 -0.2600
    106 C -35.8821 -17.5460 -4.6372 C.2 1 M_1 0.2000
    107 O -35.0881 -18.0550 -3.8612 O.2 1 M_1 -0.3900
    108 CB -38.4601 -18.1240 -2.5582 C.3 1 M_1 0.0300
    109 SG -39.2101 -19.3420 -1.4242 S.3 1 M_1 -0.1700
    110 O -39.8491 -19.8730 -4.1282 O.2 1 M_1 -0.3900
    111 CB -40.6361 -20.9300 -6.4652 C.3 1 M_1 0.0800
    112 OG -41.2231 -19.6160 -6.3822 O.3 1 M_1 -0.3900
    113 O -38.5851 -20.7710 -9.0112 O.2 1 M_1 -0.3900
    114 CB -38.8661 -16.4650 -8.8942 C.3 1 M_1 0.0400
    115 CG -38.6201 -15.5780 -10.0862 C.2 1 M_1 0.0400
    116 O1 -39.5894 -15.3190 -10.8484 O.co2 1 M_1 -0.5700
    117 O2 -37.4691 -15.1035 -10.2802 O.co2 1 M_1 -0.5700
    118 O -36.3211 -17.7810 -9.0222 O.2 1 M_1 -0.3900
    119 O -33.3361 -18.8610 -10.5802 O.2 1 M_1 -0.3900
    120 CB -33.7771 -15.2250 -12.7282 C.3 1 M_1 -0.0100
    121 CG -34.8081 -14.2520 -12.0792 C.3 1 M_1 -0.0200
    122 CD -36.2931 -14.5350 -12.4552 C.3 1 M_1 0.0600
    123 N -36.4412 -14.4206 -13.8930 N.pl3 1 M_1 -0.2700
    124 CZ -37.3945 -14.9941 -14.5655 C.2 1 M_1 0.2900
    125 N2 -38.2804 -15.7142 -13.9438 N.pl3 1 M_1 -0.2800
    126 N1 -37.5168 -14.8797 -15.8547 N.pl3 1 M_1 -0.2800
    127 O -33.6561 -16.0240 -9.6142 O.2 1 M_1 -0.3900
    128 C -29.6591 -15.4810 -8.7392 C.2 1 M_1 0.2000
    129 O -28.7531 -16.3000 -8.7642 O.2 1 M_1 -0.3900
    130 N -29.4110 -14.1692 -8.5764 N.am 1 M_1 -0.2600
    131 CA -28.0489 -13.7056 -8.3975 C.3 1 M_1 0.1300
    132 CB -27.2329 -14.7536 -7.5965 C.3 1 M_1 -0.0200
    133 C -27.4209 -13.3896 -9.7345 C.2 1 M_1 0.2000
    134 O -26.5549 -12.5336 -9.8085 O.2 1 M_1 -0.3900
    135 N -27.8396 -14.0898 -10.8038 N.am 1 M_1 -0.2600
    136 CA -27.2757 -13.8341 -12.1149 C.3 1 M_1 0.1400
    137 CB -27.0587 -15.1671 -12.8839 C.3 1 M_1 0.0000
    138 CG -25.7667 -15.1281 -13.6499 C.ar 1 M_1 -0.0400
    139 CD1 -25.5647 -14.7061 -14.9089 C.ar 1 M_1 0.0200
    140 N1 -24.2987 -14.8481 -15.2139 N.pl3 1 M_1 -0.2900
    141 CE2 -23.5937 -15.3731 -14.1909 C.ar 1 M_1 0.0600
    142 CD2 -24.4337 -15.5871 -13.1169 C.ar 1 M_1 -0.0200
    143 CE3 -23.9807 -16.1131 -11.9069 C.2 1 M_1 -0.0700
    144 CZ3 -22.6197 -16.4341 -11.8319 C.2 1 M_1 -0.0800
    145 CH2 -21.7627 -16.2261 -12.9239 C.2 1 M_1 -0.0800
    146 CZ2 -22.2367 -15.6871 -14.1279 C.2 1 M_1 -0.0400
    147 C -28.0267 -12.7751 -12.8999 C.2 1 M_1 0.2000
    148 O -29.2297 -12.6681 -12.7319 O.2 1 M_1 -0.3900
    149 N -27.3627 -12.0108 -13.7853 N.am 1 M_1 -0.2700
    150 CA -27.7904 -10.6544 -14.0675 C.3 1 M_1 0.1100
    151 CB -29.3404 -10.5344 -14.0035 C.3 1 M_1 -0.0100
    152 CG -30.0174 -11.5544 -14.9605 C.3 1 M_1 -0.0100
    153 CD -31.3794 -11.0454 -15.5075 C.3 1 M_1 0.0600
    154 N -31.9251 -12.0637 -16.3837 N.pl3 1 M_1 -0.2700
    155 CZ -33.1080 -12.0182 -16.9208 C.2 1 M_1 0.2900
    156 N2 -33.8812 -11.0088 -16.6499 N.pl3 1 M_1 -0.2800
    157 N1 -33.5683 -12.9378 -17.7161 N.pl3 1 M_1 -0.2800
    158 C -27.1234 -9.6674 -13.1425 C.2 1 M_1 0.1200
    159 O -27.6644 -8.6004 -12.8975 O.2 1 M_1 -0.3700
@<TRIPOS>BOND
     1 76 1 1
     2 76 2 1
     3 77 3 1
     4 77 4 1
     5 80 5 1
     6 81 6 1
     7 82 7 1
     8 82 8 1
     9 85 9 1
    10 85 10 1
    11 86 11 1
    12 87 12 1
    13 89 13 1
    14 90 14 1
    15 92 15 1
    16 93 16 1
    17 93 17 1
    18 94 18 1
    19 94 19 1
    20 95 20 1
    21 95 21 1
    22 98 22 1
    23 99 23 1
    24 101 24 1
    25 102 25 1
    26 104 26 1
    27 105 27 1
    28 108 28 1
    29 108 29 1
    30 109 30 1
    31 111 31 1
    32 111 32 1
    33 112 33 1
    34 114 34 1
    35 114 35 1
    36 120 36 1
    37 120 37 1
    38 121 38 1
    39 121 39 1
    40 122 40 1
    41 122 41 1
    42 123 42 1
    43 125 43 1
    44 125 44 1
    45 126 45 1
    46 126 46 1
    47 130 47 1
    48 131 48 1
    49 132 49 1
    50 132 50 1
    51 132 51 1
    52 135 52 1
    53 136 53 1
    54 137 54 1
    55 137 55 1
    56 139 56 1
    57 140 57 1
    58 143 58 1
    59 144 59 1
    60 145 60 1
    61 146 61 1
    62 149 62 1
    63 150 63 1
    64 151 64 1
    65 151 65 1
    66 152 66 1
    67 152 67 1
    68 153 68 1
    69 153 69 1
    70 154 70 1
    71 156 71 1
    72 156 72 1
    73 157 73 1
    74 157 74 1
    75 158 75 1
    76 76 77 1
    77 77 78 1
    78 78 79 2
    79 78 80 am
    80 80 81 1
    81 81 82 1
    82 81 106 1
    83 82 83 1
    84 83 84 1
    85 84 85 1
    86 85 86 1
    87 86 87 1
    88 86 128 1
    89 87 88 am
    90 88 89 1
    91 88 127 2
    92 89 90 1
    93 89 120 1
    94 90 91 am
    95 91 92 1
    96 91 119 2
    97 92 93 1
    98 92 96 1
    99 93 94 1
   100 94 95 1
   101 95 96 1
   102 96 97 am
   103 97 98 1
   104 97 118 2
   105 98 99 1
   106 98 114 1
   107 99 100 am
   108 100 101 1
   109 100 113 2
   110 101 102 1
   111 101 111 1
   112 102 103 am
   113 103 104 1
   114 103 110 2
   115 104 105 1
   116 104 108 1
   117 105 106 am
   118 106 107 2
   119 108 109 1
   120 111 112 1
   121 114 115 1
   122 115 116 ar
   123 115 117 ar
   124 120 121 1
   125 121 122 1
   126 122 123 1
   127 123 124 1
   128 124 125 1
   129 124 126 1
   130 128 129 2
   131 128 130 am
   132 130 131 1
   133 131 132 1
   134 131 133 1
   135 133 134 2
   136 133 135 am
   137 135 136 1
   138 136 137 1
   139 136 147 1
   140 137 138 1
   141 138 139 ar
   142 138 142 ar
   143 139 140 1
   144 140 141 1
   145 141 142 ar
   146 141 146 1
   147 142 143 1
   148 143 144 2
   149 144 145 2
   150 145 146 2
   151 147 148 2
   152 147 149 am
   153 149 150 1
   154 150 151 1
   155 150 158 1
   156 151 152 1
   157 152 153 1
   158 153 154 1
   159 154 155 1
   160 155 156 1
   161 155 157 1
   162 158 159 2
@<TRIPOS>SUBSTRUCTURE
     1 M_1 76 GROUP 0 A **** 0 ROOT
@<TRIPOS>SET
UNK_ATOMS STATIC ATOMS AMSOM **** Atom types guessed for these atoms
94 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 \
 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 \
 113 114 115 116 117 118 119 120 121 122 123 124 125 0 0 126 0 0 \
 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 \
 145 146 0 147 148 149 150 151 152 153 154 155 156 0 0 157 0 0 \
 158 159 0


    0 0 2

This is a remark line
molecule.res
M_1 INT 0
CORRECT OMIT DU BEG
  0.0000
   1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
   2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
   3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
   4 N15 nh M 3 2 1 1.540 111.208 180.000 -0.28000
   5 H71 hn E 4 3 2 1.030 24.027 97.396 0.00000
   6 H72 hn E 4 3 2 1.030 108.568 -139.819 0.00000
   7 C36 c2 M 4 3 2 1.300 126.497 15.034 0.29000
   8 N17 nh B 7 4 3 1.300 117.806 27.398 -0.28000
   9 H73 hn E 8 7 4 1.029 120.048 179.986 0.00000
  10 H74 hn E 8 7 4 1.031 119.993 0.035 0.00000
  11 N14 nh M 7 4 3 1.300 118.855 -152.227 -0.27000
  12 H70 hn E 11 7 4 1.029 117.764 178.794 0.00000
  13 C35 c3 M 11 7 4 1.450 124.553 -1.226 0.06000
  14 H68 h1 E 13 11 7 1.099 109.804 -66.484 0.00000
  15 H69 h1 E 13 11 7 1.101 109.741 53.918 0.00000
  16 C33 c3 M 13 11 7 1.554 108.229 173.677 -0.01000
  17 H66 hc E 16 13 11 1.100 108.687 -59.436 0.00000
  18 H67 hc E 16 13 11 1.100 108.626 59.585 0.00000
  19 C29 c3 M 16 13 11 1.553 112.581 -179.985 -0.01000
  20 H64 hc E 19 16 13 1.100 109.087 -29.700 0.00000
  21 H65 hc E 19 16 13 1.101 109.038 89.831 0.00000
  22 C10 c3 M 19 16 13 1.556 110.991 -149.976 0.11000
  23 H63 h1 E 22 19 16 1.099 107.656 62.174 0.00000
  24 C20 c B 22 19 16 1.508 111.399 179.987 0.12000
  25 H75 h4 E 24 22 19 1.089 120.019 150.017 0.00000
  26 O12 o E 24 22 19 1.221 119.930 -29.969 -0.37000
  27 N13 n M 22 19 16 1.450 110.940 -55.492 -0.27000
  28 H62 hn E 27 22 19 1.000 119.445 145.369 0.00000
  29 C19 c M 27 22 19 1.345 120.974 -34.602 0.20000
  30 O11 o E 29 27 22 1.219 121.873 32.013 -0.39000
  31 C9 c3 M 29 27 22 1.517 119.521 -150.000 0.14000
  32 H53 h1 E 31 29 27 1.100 105.510 34.100 0.00000
  33 C28 c3 3 31 29 27 1.554 114.318 -82.013 0.00000
  34 H54 hc E 33 31 29 1.100 109.228 -30.212 0.00000
  35 H55 hc E 33 31 29 1.100 109.222 -149.906 0.00000
  36 C32 cc S 33 31 29 1.503 110.491 89.973 -0.04000
  37 CD1 cd B 36 33 31 1.343 127.978 -89.993 0.02000
  38 H56 h4 E 37 36 33 1.084 125.397 0.765 0.00000
  39 N16 na B 37 36 33 1.310 109.241 -179.248 -0.29000
  40 H57 hn E 39 37 36 1.030 124.147 -179.656 0.00000
  41 CE2 ca S 39 37 36 1.349 111.763 0.325 0.06000
  42 CD2 ca S 41 39 37 1.380 109.417 -0.714 -0.02000
  43 CE3 ca B 42 41 39 1.395 122.398 -179.387 -0.07000
  44 H58 ha E 43 42 41 1.089 121.676 179.260 0.00000
  45 CZ3 ca B 43 42 41 1.400 116.647 -0.720 -0.08000
  46 H59 ha E 45 43 42 1.089 119.427 -179.659 0.00000
  47 CH2 ca B 45 43 42 1.404 121.183 0.316 -0.08000
  48 H60 ha E 47 45 43 1.089 119.374 -179.881 0.00000
  49 CZ2 ca S 47 45 43 1.402 121.249 0.139 -0.04000
  50 H61 ha E 49 47 45 1.089 121.475 179.789 0.00000
  51 N12 n M 31 29 27 1.450 113.486 150.003 -0.26000
  52 H52 hn E 51 31 29 1.000 119.821 89.975 0.00000
  53 C18 c M 51 31 29 1.345 120.375 -90.050 0.20000
  54 O10 o E 53 51 31 1.220 122.564 -0.800 -0.39000
  55 C8 c3 M 53 51 31 1.511 117.722 -179.991 0.13000
  56 H48 h1 E 55 53 51 1.101 107.814 -148.023 0.00000
  57 C27 c3 3 55 53 51 1.552 112.343 93.244 -0.02000
  58 H49 hc E 57 55 53 1.100 109.410 56.615 0.00000
  59 H50 hc E 57 55 53 1.100 109.449 -63.316 0.00000
  60 H51 hc E 57 55 53 1.100 109.487 176.648 0.00000
  61 N11 n M 55 53 51 1.450 110.412 -29.942 -0.26000
  62 H47 hn E 61 55 53 1.000 120.053 -89.973 0.00000
  63 C17 c M 61 55 53 1.345 119.978 89.941 0.20000
  64 O9 o E 63 61 55 1.222 121.310 -1.279 -0.39000
  65 C2 c3 M 63 61 55 1.516 121.632 -179.958 0.14000
  66 H11 h1 E 65 63 61 1.100 107.217 -29.753 0.00000
  67 N4 n B 65 63 61 1.469 116.003 90.035 -0.26000
  68 H12 hn E 67 65 63 1.000 120.870 18.243 0.00000
  69 C11 c S 67 65 63 1.352 118.291 -161.733 0.20000
  70 O8 o E 69 67 65 1.219 120.090 9.420 -0.39000
  71 C21 c3 M 65 63 61 1.552 108.905 -147.196 0.04000
  72 H9 h1 E 71 65 63 1.100 109.138 -168.889 0.00000
  73 H10 h1 E 71 65 63 1.100 109.158 -49.278 0.00000
  74 S1 ss M 71 65 63 1.826 110.693 70.912 -0.09000
  75 SG ss M 74 71 65 2.034 102.911 112.430 -0.09000
  76 CB c3 M 75 74 71 1.821 103.538 -92.027 0.04000
  77 H7 h1 E 76 75 74 1.100 108.882 -69.040 0.00000
  78 H8 h1 E 76 75 74 1.101 108.868 50.222 0.00000
  79 C1 c3 M 76 75 74 1.555 111.851 170.586 0.14000
  80 H6 h1 E 79 76 75 1.100 106.079 -74.723 0.00000
  81 N3 n B 79 76 75 1.450 111.179 167.593 -0.26000
  82 H5 hn E 81 79 76 1.000 119.928 -129.195 0.00000
  83 C c B 81 79 76 1.344 120.178 50.862 0.20000
  84 CA c3 3 83 81 79 1.509 117.978 -150.005 0.09000
  85 H3 h1 E 84 83 81 1.099 109.305 60.118 0.00000
  86 H4 h1 E 84 83 81 1.100 109.272 179.876 0.00000
  87 N n3 B 84 83 81 1.450 110.222 -60.062 -0.37000
  88 H1 hn E 87 84 83 1.000 120.001 -179.985 0.00000
  89 H2 hn E 87 84 83 1.000 120.018 0.041 0.00000
  90 O o E 83 81 79 1.221 122.542 29.437 -0.40000
  91 C16 c M 79 76 75 1.512 117.855 45.087 0.20000
  92 O3 o E 91 79 76 1.221 121.210 9.063 -0.39000
  93 N9 n M 91 79 76 1.350 115.972 -171.774 -0.26000
  94 H27 hn E 93 91 79 1.000 119.132 -2.338 0.00000
  95 C7 c3 M 93 91 79 1.460 121.717 177.669 0.14000
  96 H26 h1 E 95 93 91 1.100 110.050 -16.796 0.00000
  97 C23 c3 3 95 93 91 1.550 108.569 102.515 0.03000
  98 H28 h1 E 97 95 93 1.100 109.235 58.597 0.00000
  99 H29 h1 E 97 95 93 1.100 109.282 -61.148 0.00000
 100 S2 sh S 97 95 93 1.825 110.290 178.735 -0.17000
 101 H30 hs E 100 97 95 1.008 109.454 -179.980 0.00000
 102 C15 c M 95 93 91 1.514 107.468 -135.700 0.20000
 103 O4 o E 102 95 93 1.219 119.161 -128.689 -0.39000
 104 N8 n M 102 95 93 1.354 116.691 50.299 -0.26000
 105 H25 hn E 104 102 95 1.000 118.216 9.373 0.00000
 106 C6 c3 M 104 102 95 1.469 123.555 -170.660 0.15000
 107 H24 h1 E 106 104 102 1.100 107.264 -117.238 0.00000
 108 C24 c3 3 106 104 102 1.555 119.023 4.115 0.08000
 109 H31 h1 E 108 106 104 1.100 108.916 -59.650 0.00000
 110 H32 h1 E 108 106 104 1.100 108.930 -178.989 0.00000
 111 OG oh S 108 106 104 1.442 111.699 60.681 -0.39000
 112 H33 ho E 111 108 106 0.950 109.450 179.999 0.00000
 113 C14 c M 106 104 102 1.515 105.964 125.802 0.21000
 114 O5 o E 113 106 104 1.219 119.096 128.571 -0.39000
 115 N7 n M 113 106 104 1.351 117.905 -50.645 -0.26000
 116 H23 hn E 115 113 106 1.000 119.114 -5.506 0.00000
 117 C5 c3 M 115 113 106 1.469 121.749 174.505 0.14000
 118 H22 h1 E 117 115 113 1.100 108.493 62.216 0.00000
 119 C25 c3 3 117 115 113 1.560 109.973 -179.902 0.04000
 120 H34 hc E 119 117 115 1.099 108.529 62.285 0.00000
 121 H35 hc E 119 117 115 1.100 108.549 -56.599 0.00000
 122 C30 c B 119 117 115 1.506 113.218 -177.164 0.04000
 123 O1 o E 122 119 117 1.260 118.310 89.968 -0.57000
 124 O2 o E 122 119 117 1.260 119.519 -91.116 -0.57000
 125 C13 c M 117 115 113 1.526 109.909 -55.634 0.21000
 126 O6 o E 125 117 115 1.221 116.917 -76.994 -0.39000
 127 N6 n M 125 117 115 1.365 124.043 102.065 -0.25000
 128 CD c3 3 127 125 117 1.463 123.648 8.636 0.04000
 129 H20 h1 E 128 127 125 1.100 111.809 -39.632 0.00000
 130 H21 h1 E 128 127 125 1.100 111.831 83.490 0.00000
 131 CG c3 3 128 127 125 1.546 99.916 -158.090 -0.03000
 132 H18 hc E 131 128 127 1.100 111.038 84.536 0.00000
 133 H19 hc E 131 128 127 1.100 111.003 -153.489 0.00000
 134 C22 c3 B 131 128 127 1.543 103.166 -34.480 -0.01000
 135 H16 hc E 134 131 128 1.100 110.925 159.858 0.00000
 136 H17 hc E 134 131 128 1.100 110.956 -78.211 0.00000
 137 C4 c3 M 127 125 117 1.465 119.745 -166.398 0.13000
 138 H15 h1 E 137 127 125 1.100 108.781 65.942 0.00000
 139 C12 c M 137 127 125 1.514 120.153 -58.243 0.20000
 140 O7 o E 139 137 127 1.220 117.880 145.220 -0.39000
 141 N5 n M 139 137 127 1.351 120.950 -37.163 -0.26000
 142 H14 hn E 141 139 137 1.001 120.531 2.289 0.00000
 143 C3 c3 M 141 139 137 1.469 118.923 -177.690 0.13000
 144 H13 h1 E 143 141 139 1.100 106.956 61.487 0.00000
 145 C26 c3 M 143 141 139 1.559 113.908 178.596 -0.01000
 146 H36 hc E 145 143 141 1.100 108.009 -55.539 0.00000
 147 H37 hc E 145 143 141 1.100 108.014 -173.852 0.00000
 148 C31 c3 M 145 143 141 1.559 115.245 65.269 -0.02000
 149 H38 hc E 148 145 143 1.100 108.148 149.264 0.00000
 150 H39 hc E 148 145 143 1.100 108.192 30.751 0.00000
 151 C34 c3 M 148 145 143 1.558 114.615 -89.984 0.06000
 152 H40 h1 E 151 148 145 1.100 109.679 -179.903 0.00000
 153 H41 h1 E 151 148 145 1.100 109.673 59.885 0.00000
 154 N10 nh M 151 148 145 1.450 108.806 -59.983 -0.27000
 155 H42 hn E 154 151 148 1.030 118.229 -23.092 0.00000
 156 CZ c2 M 154 151 148 1.301 123.601 157.009 0.29000
 157 N1 nh B 156 154 151 1.300 122.916 179.819 -0.28000
 158 H45 hn E 157 156 154 1.030 120.003 0.236 0.00000
 159 H46 hn E 157 156 154 1.030 119.983 -179.714 0.00000
 160 N2 nh M 156 154 151 1.299 119.737 0.048 -0.28000
 161 H43 hn E 160 156 154 1.030 120.002 -179.971 0.00000
 162 H44 hn E 160 156 154 1.030 120.078 0.069 0.00000

LOOP
  CD2 C32
  CZ2 CE2
   C3 C11
   C4 C22

IMPROPER
  N14 N15 C36 N17
  C10 H75 C20 O12
   C9 N13 C19 O11
  C28 CD2 C32 CD1
  C32 H56 CD1 N16
  CE2 CD1 N16 H57
  CD2 CZ2 CE2 N16
  CE2 CE3 CD2 C32
  CD2 CZ3 CE3 H58
  CE3 CH2 CZ3 H59
  CZ3 CZ2 CH2 H60
  CE2 CH2 CZ2 H61
   C8 N12 C18 O10
   C2 N11 C17 O9
   C3 N4 C11 O8
   CA N3 C O
   C1 N9 C16 O3
   C7 N8 C15 O4
   C6 N7 C14 O5
  C25 O1 C30 O2
   C5 N6 C13 O6
   C4 N5 C12 O7
  N10 N1 CZ N2

DONE
STOP

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu