[gmx-users] atom type OXT

Mark Abraham Mark.Abraham at anu.edu.au
Tue Sep 6 14:35:09 CEST 2011


On 6/09/2011 11:39 AM, Sweta Iyer wrote:
> Hi all,
>
> I have been trying to pdbgmx my protein to obtain the gro and top files as follows:
>
> pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top -ter  -ignh
>
> However, I get an error message that states:
>
> Atom OXT in residue SER 29 was not found in rtp entry SER with 8 atoms
> while sorting atoms

We don't know what termini you are choosing (or want), so it's hard to 
help. See also http://www.gromacs.org/Documentation/How-tos/Multiple_Chains

Mark

>
> I figure from previous threads that many ppl have been facing the similar issue. I also happened to go through the discussion in the bugs page.
> This is how my pdb file looks like. Where would i have to re name my oxygen atoms in order to fix this?
>
> ATOM      1  N   LEU X   1      36.020  45.310   8.310  1     1 1.63         -0.15
> ATOM      2  CA  LEU X   1      36.400  43.890   8.240  2     1 2.03          0.10
> ATOM      3  CB  LEU X   1      37.910  43.930   7.990  6     1 1.99          0.00
> ATOM      4  CG  LEU X   1      38.320  44.530   6.640 16     1 2.03          0.00
> ATOM      5  CD1 LEU X   1      39.830  44.320   6.680 17     1 1.94          0.00
> ATOM      6  CD2 LEU X   1      37.710  43.760   5.470 17     1 1.94          0.00
> ATOM      7  C      LEU X   1      35.910  43.180   9.510  3     1 1.67          0.60
> ATOM      8  O   LEU X   1      36.680  43.050  10.460  4     1 1.38         -0.55
> ATOM      9  N   GLY X   2      34.710  42.620   9.390  1     1 1.63         -0.15
> ATOM     10  CA  GLY X   2      33.850  42.050  10.440  5     1 1.99          0.10
> ATOM     11  C   GLY X   2      34.300  40.610  10.700  3     1 1.67          0.60
> ATOM     12  O   GLY X   2      33.470  39.700  10.770  4     1 1.38         -0.55
> ATOM     13  N   ASN X   3      35.500  40.620  11.270  1     1 1.63         -0.15
> ATOM     14  CA  ASN X   3      36.180  39.350  11.510  2     1 2.03          0.10
> ATOM     15  CB  ASN X   3      37.610  39.430  10.970  6     1 1.99          0.00
> ATOM     16  CG  ASN X   3      37.560  39.470   9.440 11     1 1.67          0.55
> ATOM     17  OD1 ASN X   3      36.740  38.900   8.720 11     1 1.38         -0.55
> ATOM     18  ND2 ASN X   3      38.500  40.150   8.800 11     1 1.63          0.00
> ATOM     19  C   ASN X   3      36.140  38.770  12.930  3     1 1.67          0.60
> ATOM     20  O   ASN X   3      37.200  38.510  13.500  4     1 1.38         -0.55
> ATOM     21  N   GLY X   4      34.910  38.860  13.410  1     1 1.63         -0.15
> ATOM     22  CA  GLY X   4      34.410  38.420  14.720  5     1 1.99          0.10
> ATOM     23  C   GLY X   4      34.630  36.920  14.890  3     1 1.67          0.60
> ATOM     24  O   GLY X   4      34.060  36.200  14.070  4     1 1.38         -0.55
> ATOM     25  N   PRO X   5      35.630  36.460  15.640  1     0 1.63         -0.25
> ATOM     26  CA  PRO X   5      36.100  35.070  15.570  2     1 2.03          0.10
> ATOM     27  CB  PRO X   5      37.580  35.090  15.950  6     1 1.99          0.00
> ATOM     28  CG  PRO X   5      37.700  36.360  16.780  6     1 1.99          0.00
> ATOM     29  CD  PRO X   5      36.510  37.270  16.500  6     1 1.99          0.10
> ATOM     30  C   PRO X   5      35.290  34.130  16.470  3     0 1.67          0.60
> ATOM     31  O   PRO X   5      35.300  34.320  17.690  4     0 1.38         -0.55
> ATOM     32  N   ILE X   6      34.630  33.150  15.870  1     1 1.63         -0.15
> ATOM     33  CA  ILE X   6      33.650  32.240  16.500  2     1 2.03          0.10
> ATOM     34  CB  ILE X   6      33.090  31.180  15.550  6     1 2.03          0.00
> ATOM     35  CG1 ILE X   6      32.320  31.810  14.400 16     1 1.99          0.00
> ATOM     36  CG2 ILE X   6      32.170  30.220  16.310 17     1 1.94          0.00
> ATOM     37  CD  ILE X   6      31.910  30.940  13.210 17     1 1.94          0.00
> ATOM     38  C   ILE X   6      34.280  31.620  17.750  3     0 1.67          0.60
> ATOM     39  O   ILE X   6      33.860  31.920  18.870  4     0 1.38         -0.55
> ATOM     40  N   LEU X   7      35.460  31.050  17.520  1     0 1.63         -0.15
> ATOM     41  CA  LEU X   7      36.260  30.330  18.520  2     0 2.03          0.10
> ATOM     42  CB  LEU X   7      37.480  29.600  17.970  6     1 1.99          0.00
> ATOM     43  CG  LEU X   7      37.050  28.470  17.030 16     1 2.03          0.00
> ATOM     44  CD1 LEU X   7      38.310  28.200  16.220 17     1 1.94          0.00
> ATOM     45  CD2 LEU X   7      36.700  27.200  17.810 17     1 1.94          0.00
> ATOM     46  C   LEU X   7      36.640  31.270  19.670  3     0 1.67          0.60
> ATOM     47  O   LEU X   7      36.630  30.820  20.820  4     0 1.38         -0.55
> ATOM     48  N   ASN X   8      36.880  32.550  19.390  1     0 1.63         -0.15
> ATOM     49  CA  ASN X   8      37.240  33.460  20.490  2     0 2.03          0.10
> ATOM     50  CB  ASN X   8      38.030  34.660  19.970  6     1 1.99          0.00
> ATOM     51  CG  ASN X   8      39.510  34.340  19.760 11     1 1.67          0.55
> ATOM     52  OD1 ASN X   8      40.030  33.230  19.760 11     1 1.38         -0.55
> ATOM     53  ND2 ASN X   8      40.270  35.420  19.930 11     1 1.63          0.00
> ATOM     54  C   ASN X   8      36.020  33.870  21.320  3     0 1.67          0.60
> ATOM     55  O   ASN X   8      36.130  33.850  22.540  4     0 1.38         -0.55
> ATOM     56  N   VAL X   9      34.890  34.170  20.680  1     0 1.63         -0.15
> ATOM     57  CA  VAL X   9      33.560  34.270  21.290  2     0 2.03          0.10
> ATOM     58  CB  VAL X   9      32.530  34.570  20.200  6     0 2.03          0.00
> ATOM     59  CG1 VAL X   9      31.090  34.750  20.670 17     1 1.94          0.00
> ATOM     60  CG2 VAL X   9      32.860  35.820  19.390 17     1 1.94          0.00
> ATOM     61  C   VAL X   9      33.130  33.020  22.070  3     0 1.67          0.60
> ATOM     62  O   VAL X   9      32.780  33.100  23.250  4     0 1.38         -0.55
> ATOM     63  N   LEU X  10      33.430  31.820  21.590  1     0 1.63         -0.15
> ATOM     64  CA  LEU X  10      33.320  30.550  22.320  2     0 2.03          0.10
> ATOM     65  CB  LEU X  10      33.560  29.280  21.500  6     1 1.99          0.00
> ATOM     66  CG  LEU X  10      32.440  29.000  20.490 16     0 2.03          0.00
> ATOM     67  CD1 LEU X  10      32.740  27.690  19.750 17     1 1.94          0.00
> ATOM     68  CD2 LEU X  10      31.050  28.950  21.110 17     1 1.94          0.00
> ATOM     69  C   LEU X  10      34.080  30.460  23.650  3     1 1.67          0.60
> ATOM     70  O   LEU X  10      33.470  29.940  24.580  4     1 1.38         -0.55
> ATOM     71  N   VAL X  11      35.300  30.990  23.660  1     0 1.63         -0.15
> ATOM     72  CA  VAL X  11      36.130  31.100  24.870  2     1 2.03          0.10
> ATOM     73  CB  VAL X  11      37.620  31.170  24.520  6     1 2.03          0.00
> ATOM     74  CG1 VAL X  11      38.460  31.040  25.800 17     1 1.94          0.00
> ATOM     75  CG2 VAL X  11      38.050  29.940  23.720 17     1 1.94          0.00
> ATOM     76  C   VAL X  11      35.650  32.210  25.790  3     0 1.67          0.60
> ATOM     77  O   VAL X  11      35.670  32.040  27.010  4     0 1.38         -0.55
> ATOM     78  N   VAL X  12      35.230  33.330  25.200  1     0 1.63         -0.15
> ATOM     79  CA  VAL X  12      34.590  34.450  25.910  2     1 2.03          0.10
> ATOM     80  CB  VAL X  12      34.320  35.780  25.200  6     1 2.03          0.00
> ATOM     81  CG1 VAL X  12      33.770  36.830  26.160 17     1 1.94          0.00
> ATOM     82  CG2 VAL X  12      35.530  36.270  24.410 17     1 1.94          0.00
> ATOM     83  C   VAL X  12      33.420  33.940  26.750  3     0 1.67          0.60
> ATOM     84  O   VAL X  12      33.330  34.260  27.930  4     0 1.38         -0.55
> ATOM     85  N   LEU X  13      32.520  33.210  26.100  1     0 1.63         -0.15
> ATOM     86  CA  LEU X  13      31.360  32.530  26.700  2     0 2.03          0.10
> ATOM     87  CB  LEU X  13      30.520  31.890  25.580  6     1 1.99          0.00
> ATOM     88  CG  LEU X  13      29.860  32.940  24.690 16     0 2.03          0.00
> ATOM     89  CD1 LEU X  13      29.270  32.390  23.390 17     1 1.94          0.00
> ATOM     90  CD2 LEU X  13      28.820  33.750  25.460 17     1 1.94          0.00
> ATOM     91  C   LEU X  13      31.710  31.460  27.730  3     0 1.67          0.60
> ATOM     92  O   LEU X  13      31.230  31.510  28.860  4     0 1.38         -0.55
> ATOM     93  N   GLY X  14      32.750  30.710  27.350  1     1 1.63         -0.15
> ATOM     94  CA  GLY X  14      33.460  29.880  28.330  5     1 1.99          0.10
> ATOM     95  C   GLY X  14      33.880  30.510  29.650  3     1 1.67          0.60
> ATOM     96  O   GLY X  14      33.440  30.110  30.730  4     0 1.38         -0.55
> ATOM     97  N   VAL X  15      34.660  31.580  29.500  1     0 1.63         -0.15
> ATOM     98  CA  VAL X  15      35.070  32.460  30.600  2     0 2.03          0.10
> ATOM     99  CB  VAL X  15      36.180  33.350  30.030  6     1 2.03          0.00
> ATOM    100  CG1 VAL X  15      36.760  34.280  31.100 17     1 1.94          0.00
> ATOM    101  CG2 VAL X  15      37.370  32.500  29.570 17     1 1.94          0.00
> ATOM    102  C   VAL X  15      34.000  33.250  31.350  3     0 1.67          0.60
> ATOM    103  O   VAL X  15      33.940  33.260  32.570  4     1 1.38         -0.55
> ATOM    104  N   VAL X  16      32.980  33.680  30.600  1     0 1.63         -0.15
> ATOM    105  CA  VAL X  16      31.800  34.290  31.220  2     1 2.03          0.10
> ATOM    106  CB  VAL X  16      30.920  34.810  30.080  6     0 2.03          0.00
> ATOM    107  CG1 VAL X  16      29.450  35.110  30.370 17     1 1.94          0.00
> ATOM    108  CG2 VAL X  16      31.480  36.110  29.490 17     1 1.94          0.00
> ATOM    109  C   VAL X  16      31.000  33.300  32.090  3     0 1.67          0.60
> ATOM    110  O   VAL X  16      30.540  33.590  33.190  4     1 1.38         -0.55
> ATOM    111  N   LEU X  17      30.900  32.060  31.630  1     0 1.63         -0.15
> ATOM    112  CA  LEU X  17      30.330  30.950  32.410  2     0 2.03          0.10
> ATOM    113  CB  LEU X  17      30.050  29.730  31.540  6     1 1.99          0.00
> ATOM    114  CG  LEU X  17      28.930  29.950  30.520 16     1 2.03          0.00
> ATOM    115  CD1 LEU X  17      29.040  28.850  29.460 17     1 1.94          0.00
> ATOM    116  CD2 LEU X  17      27.580  29.680  31.190 17     1 1.94          0.00
> ATOM    117  C   LEU X  17      31.040  30.410  33.660  3     0 1.67          0.60
> ATOM    118  O   LEU X  17      30.470  30.320  34.740  4     0 1.38         -0.55
> ATOM    119  N   LEU X  18      32.350  30.190  33.590  1     0 1.63         -0.15
> ATOM    120  CA  LEU X  18      33.180  29.960  34.780  2     0 2.03          0.10
> ATOM    121  CB  LEU X  18      34.610  29.730  34.270  6     1 1.99          0.00
> ATOM    122  CG  LEU X  18      34.810  28.480  33.400 16     1 2.03          0.00
> ATOM    123  CD1 LEU X  18      36.250  28.480  32.880 17     1 1.94          0.00
> ATOM    124  CD2 LEU X  18      34.600  27.170  34.160 17     1 1.94          0.00
> ATOM    125  C   LEU X  18      33.170  31.140  35.750  3     1 1.67          0.60
> ATOM    126  O   LEU X  18      32.870  30.940  36.920  4     0 1.38         -0.55
> ATOM    127  N   GLY X  19      33.080  32.370  35.240  1     1 1.63         -0.15
> ATOM    128  CA  GLY X  19      32.750  33.600  35.980  5     1 1.99          0.10
> ATOM    129  C   GLY X  19      31.490  33.480  36.850  3     1 1.67          0.60
> ATOM    130  O   GLY X  19      31.610  33.290  38.060  4     0 1.38         -0.55
> ATOM    131  N   GLN X  20      30.380  33.290  36.150  1     1 1.63         -0.15
> ATOM    132  CA  GLN X  20      29.130  32.960  36.840  2     1 2.03          0.10
> ATOM    133  CB  GLN X  20      28.050  32.550  35.840  6     0 1.99          0.00
> ATOM    134  CG  GLN X  20      27.690  33.670  34.860 16     1 1.99          0.00
> ATOM    135  CD  GLN X  20      26.480  33.090  34.130 11     1 1.67          0.55
> ATOM    136  OE1 GLN X  20      25.330  33.310  34.500 11     1 1.38         -0.55
> ATOM    137  NE2 GLN X  20      26.640  32.490  32.950 11     1 1.63          0.00
> ATOM    138  C   GLN X  20      29.230  31.850  37.880  3     0 1.67          0.60
> ATOM    139  O   GLN X  20      28.860  32.060  39.030  4     0 1.38         -0.55
> ATOM    140  N   PHE X  21      29.860  30.730  37.530  1     0 1.63         -0.15
> ATOM    141  CA  PHE X  21      30.140  29.640  38.480  2     0 2.03          0.10
> ATOM    142  CB  PHE X  21      30.570  28.370  37.740  6     1 1.99          0.00
> ATOM    143  CG  PHE X  21      29.430  27.820  36.880 16     1 1.82          0.00
> ATOM    144  CD1 PHE X  21      29.660  27.540  35.540 16     1 1.78          0.00
> ATOM    145  CD2 PHE X  21      28.130  27.760  37.370 16     1 1.78          0.00
> ATOM    146  CE1 PHE X  21      28.650  27.150  34.660 16     1 1.78          0.00
> ATOM    147  CE2 PHE X  21      27.140  27.230  36.560 16     1 1.78          0.00
> ATOM    148  CZ  PHE X  21      27.400  26.930  35.230 16     1 1.78          0.00
> ATOM    149  C   PHE X  21      31.000  29.930  39.710  3     1 1.67          0.60
> ATOM    150  O   PHE X  21      30.570  29.570  40.800  4     1 1.38         -0.55
> ATOM    151  N   VAL X  22      32.130  30.620  39.540  1     0 1.63         -0.15
> ATOM    152  CA  VAL X  22      33.000  31.100  40.620  2     1 2.03          0.10
> ATOM    153  CB  VAL X  22      34.330  31.720  40.170  6     1 2.03          0.00
> ATOM    154  CG1 VAL X  22      35.240  32.310  41.250 17     1 1.94          0.00
> ATOM    155  CG2 VAL X  22      35.120  30.560  39.570 17     1 1.94          0.00
> ATOM    156  C   VAL X  22      32.220  31.930  41.640  3     0 1.67          0.60
> ATOM    157  O   VAL X  22      32.440  31.830  42.840  4     1 1.38         -0.55
> ATOM    158  N   VAL X  23      31.290  32.770  41.210  1     0 1.63         -0.15
> ATOM    159  CA  VAL X  23      30.420  33.640  42.020  2     1 2.03          0.10
> ATOM    160  CB  VAL X  23      29.930  34.910  41.330  6     1 2.03          0.00
> ATOM    161  CG1 VAL X  23      29.830  35.960  42.440 17     1 1.94          0.00
> ATOM    162  CG2 VAL X  23      30.790  35.550  40.230 17     1 1.94          0.00
> ATOM    163  C   VAL X  23      29.150  32.930  42.510  3     0 1.67          0.60
> ATOM    164  O   VAL X  23      28.630  33.100  43.610  4     1 1.38         -0.55
> ATOM    165  N   ARG X  24      28.510  32.060  41.730  1     0 1.63         -0.15
> ATOM    166  CA  ARG X  24      27.330  31.320  42.200  2     1 2.03          0.10
> ATOM    167  CB  ARG X  24      26.440  31.070  40.980  6     1 1.99          0.00
> ATOM    168  CG  ARG X  24      25.760  32.350  40.480 16     1 1.99          0.00
> ATOM    169  CD  ARG X  24      25.060  32.250  39.120 12     1 1.99          0.10
> ATOM    170  NE  ARG X  24      24.200  33.420  38.900 12     1 1.63         -0.10
> ATOM    171  CZ  ARG X  24      23.420  33.690  37.850 10     1 1.67          0.50
> ATOM    172  NH1 ARG X  24      23.310  32.810  36.850 10     1 1.63          0.25
> ATOM    173  NH2 ARG X  24      22.630  34.770  37.830 10     1 1.63          0.25
> ATOM    174  C   ARG X  24      27.620  30.020  42.950  3     0 1.67          0.60
> ATOM    175  O   ARG X  24      27.430  28.920  42.440  4     1 1.38         -0.55
> ATOM    176  N   ARG X  25      27.640  30.280  44.260  1     1 1.63         -0.15
> ATOM    177  CA  ARG X  25      27.950  29.310  45.320  2     1 2.03          0.10
> ATOM    178  CB  ARG X  25      28.970  29.860  46.330  6     1 1.99          0.00
> ATOM    179  CG  ARG X  25      30.150  30.420  45.530 16     1 1.99          0.00
> ATOM    180  CD  ARG X  25      31.200  30.890  46.530 12     1 1.99          0.10
> ATOM    181  NE  ARG X  25      32.490  31.070  45.850 12     1 1.63         -0.10
> ATOM    182  CZ  ARG X  25      33.680  30.670  46.320 10     1 1.67          0.50
> ATOM    183  NH1 ARG X  25      33.760  30.230  47.590 10     1 1.63          0.25
> ATOM    184  NH2 ARG X  25      34.690  31.380  45.790 10     1 1.63          0.25
> ATOM    185  C   ARG X  25      26.850  28.560  46.080  3     0 1.67          0.60
> ATOM    186  O   ARG X  25      26.210  29.090  46.990  4     1 1.38         -0.55
> ATOM    187  N   PHE X  26      26.930  27.250  45.850  1     0 1.63         -0.15
> ATOM    188  CA  PHE X  26      26.030  26.230  46.390  2     1 2.03          0.10
> ATOM    189  CB  PHE X  26      25.260  25.610  45.220  6     1 1.99          0.00
> ATOM    190  CG  PHE X  26      24.390  26.620  44.460 16     1 1.82          0.00
> ATOM    191  CD1 PHE X  26      24.770  27.160  43.240 16     1 1.78          0.00
> ATOM    192  CD2 PHE X  26      23.330  27.200  45.150 16     1 1.78          0.00
> ATOM    193  CE1 PHE X  26      24.020  28.190  42.700 16     1 1.78          0.00
> ATOM    194  CE2 PHE X  26      22.620  28.290  44.660 16     1 1.78          0.00
> ATOM    195  CZ  PHE X  26      22.960  28.770  43.400 16     1 1.78          0.00
> ATOM    196  C   PHE X  26      26.600  25.150  47.310  3     1 1.67          0.60
> ATOM    197  O   PHE X  26      25.800  24.280  47.650  4     1 1.38         -0.55
> ATOM    198  N   PHE X  27      27.670  25.540  47.990  1     0 1.63         -0.15
> ATOM    199  CA  PHE X  27      28.390  24.510  48.760  2     1 2.03          0.10
> ATOM    200  CB  PHE X  27      29.640  23.990  48.040  6     1 1.99          0.00
> ATOM    201  CG  PHE X  27      29.110  23.120  46.900 16     1 1.82          0.00
> ATOM    202  CD1 PHE X  27      29.330  23.690  45.650 16     1 1.78          0.00
> ATOM    203  CD2 PHE X  27      28.460  21.900  46.980 16     1 1.78          0.00
> ATOM    204  CE1 PHE X  27      28.990  22.990  44.500 16     1 1.78          0.00
> ATOM    205  CE2 PHE X  27      28.100  21.230  45.820 16     1 1.78          0.00
> ATOM    206  CZ  PHE X  27      28.410  21.730  44.560 16     1 1.78          0.00
> ATOM    207  C   PHE X  27      28.820  24.970  50.150  3     1 1.67          0.60
> ATOM    208  O   PHE X  27      30.010  24.930  50.480  4     1 1.38         -0.55
> ATOM    209  N   LYS X  28      27.760  25.150  50.930  1     1 1.63         -0.15
> ATOM    210  CA  LYS X  28      27.790  25.560  52.340  2     1 2.03          0.10
> ATOM    211  CB  LYS X  28      26.730  26.640  52.600  6     1 1.99          0.00
> ATOM    212  CG  LYS X  28      26.960  27.910  51.780 16     1 1.99          0.00
> ATOM    213  CD  LYS X  28      25.920  28.920  52.270  8     1 1.99          0.00
> ATOM    214  CE  LYS X  28      26.150  30.140  51.380  7     1 1.99          0.25
> ATOM    215  NZ  LYS X  28      25.160  31.210  51.480  7     1 1.47          0.75
> ATOM    216  C   LYS X  28      27.640  24.380  53.290  3     1 1.67          0.60
> ATOM    217  O   LYS X  28      26.580  23.780  53.480  4     1 1.38         -0.55
> ATOM    218  N   SER X  29      28.840  23.860  53.540  1     1 1.63         -0.15
> ATOM    219  CA  SER X  29      29.220  22.840  54.530  2     1 2.03          0.10
> ATOM    220  CB  SER X  29      28.700  21.460  54.150 13     1 1.99          0.25
> ATOM    221  OG  SER X  29      28.820  21.100  52.770 13     1 1.38         -0.25
> ATOM    222  C   SER X  29      30.710  22.820  54.890  3     1 1.67          0.60
> ATOM    223  O1  SER X  29      31.520  23.540  54.270  0     1 1.90          0.00
> ATOM    224  O2  SER X  29      30.930  22.020  55.820  0     1 1.90          0.00
> ATOM      1  N   LEU X   1      57.968  40.318  10.478  1     1 1.63         -0.15
> ATOM      2  CA  LEU X   1      56.538  40.454  10.158  2     1 2.03          0.10
> ATOM      3  CB  LEU X   1      56.345  39.528   8.954  6     1 1.99          0.00
> ATOM      4  CG  LEU X   1      57.090  39.961   7.687 16     1 2.03          0.00
> ATOM      5  CD1 LEU X   1      56.604  38.910   6.695 17     1 1.94          0.00
> ATOM      6  CD2 LEU X   1      56.666  41.356   7.230 17     1 1.94          0.00
> ATOM      7  C   LEU X   1      55.715  40.158  11.420  3     1 1.67          0.60
> ATOM      8  O   LEU X   1      55.279  39.023  11.599  4     1 1.38         -0.55
> ATOM      9  N   GLY X   2      55.414  41.237  12.137  1     1 1.63         -0.15
> ATOM     10  CA  GLY X   2      54.833  41.313  13.488  5     1 1.99          0.10
> ATOM     11  C   GLY X   2      53.312  41.190  13.364  3     1 1.67          0.60
> ATOM     12  O   GLY X   2      52.572  41.969  13.969  4     1 1.38         -0.55
> ATOM     13  N   ASN X   3      53.001  39.958  12.974  1     1 1.63         -0.15
> ATOM     14  CA  ASN X   3      51.606  39.640  12.681  2     1 2.03          0.10
> ATOM     15  CB  ASN X   3      51.518  38.950  11.318  6     1 1.99          0.00
> ATOM     16  CG  ASN X   3      51.838  39.972  10.224 11     1 1.67          0.55
> ATOM     17  OD1 ASN X   3      51.565  41.173  10.242 11     1 1.38         -0.55
> ATOM     18  ND2 ASN X   3      52.438  39.544   9.123 11     1 1.63          0.00
> ATOM     19  C   ASN X   3      50.799  38.892  13.751  3     1 1.67          0.60
> ATOM     20  O   ASN X   3      50.252  37.830  13.453  4     1 1.38         -0.55
> ATOM     21  N   GLY X   4      51.026  39.435  14.936  1     1 1.63         -0.15
> ATOM     22  CA  GLY X   4      50.458  39.051  16.236  5     1 1.99          0.10
> ATOM     23  C   GLY X   4      48.937  39.166  16.201  3     1 1.67          0.60
> ATOM     24  O   GLY X   4      48.492  40.292  15.975  4     1 1.38         -0.55
> ATOM     25  N   PRO X   5      48.176  38.081  16.075  1     0 1.63         -0.25
> ATOM     26  CA  PRO X   5      46.759  38.145  15.695  2     1 2.03          0.10
> ATOM     27  CB  PRO X   5      46.440  36.835  14.976  6     1 1.99          0.00
> ATOM     28  CG  PRO X   5      47.498  35.885  15.517  6     1 1.99          0.00
> ATOM     29  CD  PRO X   5      48.645  36.685  16.122  6     1 1.99          0.10
> ATOM     30  C   PRO X   5      45.838  38.378  16.898  3     0 1.67          0.60
> ATOM     31  O   PRO X   5      45.802  37.527  17.792  4     0 1.38         -0.55
> ATOM     32  N   ILE X   6      45.118  39.490  16.893  1     1 1.63         -0.15
> ATOM     33  CA  ILE X   6      44.305  40.013  18.012  2     1 2.03          0.10
> ATOM     34  CB  ILE X   6      43.552  41.302  17.681  6     1 2.03          0.00
> ATOM     35  CG1 ILE X   6      44.507  42.441  17.358 16     1 1.99          0.00
> ATOM     36  CG2 ILE X   6      42.657  41.709  18.855 17     1 1.94          0.00
> ATOM     37  CD  ILE X   6      43.953  43.731  16.750 17     1 1.94          0.00
> ATOM     38  C   ILE X   6      43.368  38.906  18.503  3     0 1.67          0.60
> ATOM     39  O   ILE X   6      43.535  38.400  19.615  4     0 1.38         -0.55
> ATOM     40  N   LEU X   7      42.642  38.359  17.532  1     0 1.63         -0.15
> ATOM     41  CA  LEU X   7      41.621  37.319  17.723  2     0 2.03          0.10
> ATOM     42  CB  LEU X   7      40.790  36.993  16.488  6     1 1.99          0.00
> ATOM     43  CG  LEU X   7      39.944  38.201  16.076 16     1 2.03          0.00
> ATOM     44  CD1 LEU X   7      39.596  37.897  14.625 17     1 1.94          0.00
> ATOM     45  CD2 LEU X   7      38.641  38.267  16.877 17     1 1.94          0.00
> ATOM     46  C   LEU X   7      42.255  36.059  18.323  3     0 1.67          0.60
> ATOM     47  O   LEU X   7      41.617  35.432  19.174  4     0 1.38         -0.55
> ATOM     48  N   ASN X   8      43.499  35.743  17.964  1     0 1.63         -0.15
> ATOM     49  CA  ASN X   8      44.117  34.537  18.540  2     0 2.03          0.10
> ATOM     50  CB  ASN X   8      45.225  34.005  17.633  6     1 1.99          0.00
> ATOM     51  CG  ASN X   8      44.682  33.166  16.476 11     1 1.67          0.55
> ATOM     52  OD1 ASN X   8      43.514  33.078  16.116 11     1 1.38         -0.55
> ATOM     53  ND2 ASN X   8      45.557  32.236  16.097 11     1 1.63          0.00
> ATOM     54  C   ASN X   8      44.588  34.763  19.979  3     0 1.67          0.60
> ATOM     55  O   ASN X   8      44.331  33.895  20.805  4     0 1.38         -0.55
> ATOM     56  N   VAL X   9      45.199  35.911  20.273  1     0 1.63         -0.15
> ATOM     57  CA  VAL X   9      45.430  36.438  21.622  2     0 2.03          0.10
> ATOM     58  CB  VAL X   9      46.103  37.808  21.516  6     0 2.03          0.00
> ATOM     59  CG1 VAL X   9      46.457  38.484  22.836 17     1 1.94          0.00
> ATOM     60  CG2 VAL X   9      47.396  37.780  20.706 17     1 1.94          0.00
> ATOM     61  C   VAL X   9      44.162  36.556  22.477  3     0 1.67          0.60
> ATOM     62  O   VAL X   9      44.093  36.017  23.584  4     0 1.38         -0.55
> ATOM     63  N   LEU X  10      43.032  36.961  21.911  1     0 1.63         -0.15
> ATOM     64  CA  LEU X  10      41.694  36.888  22.513  2     0 2.03          0.10
> ATOM     65  CB  LEU X  10      40.569  37.575  21.736  6     1 1.99          0.00
> ATOM     66  CG  LEU X  10      40.683  39.105  21.745 16     0 2.03          0.00
> ATOM     67  CD1 LEU X  10      39.493  39.707  20.986 17     1 1.94          0.00
> ATOM     68  CD2 LEU X  10      40.778  39.707  23.141 17     1 1.94          0.00
> ATOM     69  C   LEU X  10      41.231  35.502  22.980  3     1 1.67          0.60
> ATOM     70  O   LEU X  10      40.674  35.465  24.074  4     1 1.38         -0.55
> ATOM     71  N   VAL X  11      41.519  34.489  22.168  1     0 1.63         -0.15
> ATOM     72  CA  VAL X  11      41.257  33.079  22.501  2     1 2.03          0.10
> ATOM     73  CB  VAL X  11      41.115  32.225  21.237  6     1 2.03          0.00
> ATOM     74  CG1 VAL X  11      40.607  30.824  21.612 17     1 1.94          0.00
> ATOM     75  CG2 VAL X  11      39.989  32.753  20.346 17     1 1.94          0.00
> ATOM     76  C   VAL X  11      42.254  32.539  23.512  3     0 1.67          0.60
> ATOM     77  O   VAL X  11      41.869  31.774  24.397  4     0 1.38         -0.55
> ATOM     78  N   VAL X  12      43.519  32.938  23.370  1     0 1.63         -0.15
> ATOM     79  CA  VAL X  12      44.593  32.647  24.335  2     1 2.03          0.10
> ATOM     80  CB  VAL X  12      46.054  32.963  24.004  6     1 2.03          0.00
> ATOM     81  CG1 VAL X  12      46.999  32.462  25.092 17     1 1.94          0.00
> ATOM     82  CG2 VAL X  12      46.448  32.488  22.609 17     1 1.94          0.00
> ATOM     83  C   VAL X  12      44.164  33.066  25.740  3     0 1.67          0.60
> ATOM     84  O   VAL X  12      44.279  32.280  26.674  4     0 1.38         -0.55
> ATOM     85  N   LEU X  13      43.739  34.319  25.863  1     0 1.63         -0.15
> ATOM     86  CA  LEU X  13      43.186  34.930  27.083  2     0 2.03          0.10
> ATOM     87  CB  LEU X  13      42.921  36.423  26.819  6     1 1.99          0.00
> ATOM     88  CG  LEU X  13      44.216  37.206  26.617 16     0 2.03          0.00
> ATOM     89  CD1 LEU X  13      44.023  38.615  26.052 17     1 1.94          0.00
> ATOM     90  CD2 LEU X  13      45.052  37.241  27.894 17     1 1.94          0.00
> ATOM     91  C   LEU X  13      41.904  34.282  27.598  3     0 1.67          0.60
> ATOM     92  O   LEU X  13      41.839  33.876  28.755  4     0 1.38         -0.55
> ATOM     93  N   GLY X  14      41.057  33.978  26.609  1     1 1.63         -0.15
> ATOM     94  CA  GLY X  14      39.950  33.044  26.845  5     1 1.99          0.10
> ATOM     95  C   GLY X  14      40.247  31.724  27.540  3     1 1.67          0.60
> ATOM     96  O   GLY X  14      39.748  31.437  28.631  4     0 1.38         -0.55
> ATOM     97  N   VAL X  15      41.165  30.991  26.912  1     0 1.63         -0.15
> ATOM     98  CA  VAL X  15      41.745  29.757  27.453  2     0 2.03          0.10
> ATOM     99  CB  VAL X  15      42.504  29.108  26.290  6     1 2.03          0.00
> ATOM    100  CG1 VAL X  15      43.106  27.759  26.695 17     1 1.94          0.00
> ATOM    101  CG2 VAL X  15      41.546  28.774  25.141 17     1 1.94          0.00
> ATOM    102  C   VAL X  15      42.571  29.831  28.735  3     0 1.67          0.60
> ATOM    103  O   VAL X  15      42.374  29.076  29.676  4     1 1.38         -0.55
> ATOM    104  N   VAL X  16      43.307  30.938  28.875  1     0 1.63         -0.15
> ATOM    105  CA  VAL X  16      44.002  31.222  30.134  2     1 2.03          0.10
> ATOM    106  CB  VAL X  16      44.869  32.461  29.891  6     0 2.03          0.00
> ATOM    107  CG1 VAL X  16      45.376  33.245  31.100 17     1 1.94          0.00
> ATOM    108  CG2 VAL X  16      46.128  32.113  29.089 17     1 1.94          0.00
> ATOM    109  C   VAL X  16      43.036  31.479  31.307  3     0 1.67          0.60
> ATOM    110  O   VAL X  16      43.205  31.018  32.432  4     1 1.38         -0.55
> ATOM    111  N   LEU X  17      41.938  32.167  31.026  1     0 1.63         -0.15
> ATOM    112  CA  LEU X  17      40.830  32.350  31.977  2     0 2.03          0.10
> ATOM    113  CB  LEU X  17      39.856  33.428  31.514  6     1 1.99          0.00
> ATOM    114  CG  LEU X  17      40.456  34.836  31.520 16     1 2.03          0.00
> ATOM    115  CD1 LEU X  17      39.561  35.729  30.655 17     1 1.94          0.00
> ATOM    116  CD2 LEU X  17      40.322  35.433  32.924 17     1 1.94          0.00
> ATOM    117  C   LEU X  17      39.955  31.166  32.415  3     0 1.67          0.60
> ATOM    118  O   LEU X  17      39.780  30.893  33.595  4     0 1.38         -0.55
> ATOM    119  N   LEU X  18      39.515  30.332  31.477  1     0 1.63         -0.15
> ATOM    120  CA  LEU X  18      38.929  29.022  31.792  2     0 2.03          0.10
> ATOM    121  CB  LEU X  18      38.535  28.392  30.448  6     1 1.99          0.00
> ATOM    122  CG  LEU X  18      37.445  29.135  29.661 16     1 2.03          0.00
> ATOM    123  CD1 LEU X  18      37.275  28.444  28.305 17     1 1.94          0.00
> ATOM    124  CD2 LEU X  18      36.082  29.124  30.353 17     1 1.94          0.00
> ATOM    125  C   LEU X  18      39.898  28.096  32.524  3     1 1.67          0.60
> ATOM    126  O   LEU X  18      39.551  27.600  33.587  4     0 1.38         -0.55
> ATOM    127  N   GLY X  19      41.195  28.179  32.218  1     1 1.63         -0.15
> ATOM    128  CA  GLY X  19      42.313  27.619  32.997  5     1 1.99          0.10
> ATOM    129  C   GLY X  19      42.272  27.983  34.488  3     1 1.67          0.60
> ATOM    130  O   GLY X  19      41.851  27.157  35.298  4     0 1.38         -0.55
> ATOM    131  N   GLN X  20      42.416  29.280  34.720  1     1 1.63         -0.15
> ATOM    132  CA  GLN X  20      42.203  29.808  36.071  2     1 2.03          0.10
> ATOM    133  CB  GLN X  20      42.182  31.336  36.059  6     0 1.99          0.00
> ATOM    134  CG  GLN X  20      43.506  31.945  35.589 16     1 1.99          0.00
> ATOM    135  CD  GLN X  20      43.296  33.434  35.863 11     1 1.67          0.55
> ATOM    136  OE1 GLN X  20      43.654  33.958  36.914 11     1 1.38         -0.55
> ATOM    137  NE2 GLN X  20      42.897  34.241  34.879 11     1 1.63          0.00
> ATOM    138  C   GLN X  20      40.926  29.343  36.761  3     0 1.67          0.60
> ATOM    139  O   GLN X  20      40.992  28.804  37.861  4     0 1.38         -0.55
> ATOM    140  N   PHE X  21      39.790  29.406  36.068  1     0 1.63         -0.15
> ATOM    141  CA  PHE X  21      38.516  28.866  36.571  2     0 2.03          0.10
> ATOM    142  CB  PHE X  21      37.341  29.365  35.724  6     1 1.99          0.00
> ATOM    143  CG  PHE X  21      37.171  30.880  35.856 16     1 1.82          0.00
> ATOM    144  CD1 PHE X  21      37.097  31.660  34.710 16     1 1.78          0.00
> ATOM    145  CD2 PHE X  21      37.264  31.505  37.094 16     1 1.78          0.00
> ATOM    146  CE1 PHE X  21      37.062  33.054  34.740 16     1 1.78          0.00
> ATOM    147  CE2 PHE X  21      37.077  32.875  37.161 16     1 1.78          0.00
> ATOM    148  CZ  PHE X  21      36.976  33.632  36.002 16     1 1.78          0.00
> ATOM    149  C   PHE X  21      38.420  27.376  36.900  3     1 1.67          0.60
> ATOM    150  O   PHE X  21      37.956  27.065  37.991  4     1 1.38         -0.55
> ATOM    151  N   VAL X  22      38.910  26.503  36.017  1     0 1.63         -0.15
> ATOM    152  CA  VAL X  22      39.023  25.056  36.230  2     1 2.03          0.10
> ATOM    153  CB  VAL X  22      39.459  24.240  35.005  6     1 2.03          0.00
> ATOM    154  CG1 VAL X  22      39.671  22.736  35.191 17     1 1.94          0.00
> ATOM    155  CG2 VAL X  22      38.300  24.363  34.019 17     1 1.94          0.00
> ATOM    156  C   VAL X  22      39.786  24.736  37.515  3     0 1.67          0.60
> ATOM    157  O   VAL X  22      39.435  23.823  38.251  4     1 1.38         -0.55
> ATOM    158  N   VAL X  23      40.845  25.467  37.833  1     0 1.63         -0.15
> ATOM    159  CA  VAL X  23      41.701  25.338  39.025  2     1 2.03          0.10
> ATOM    160  CB  VAL X  23      43.142  25.814  38.857  6     1 2.03          0.00
> ATOM    161  CG1 VAL X  23      43.977  24.894  39.752 17     1 1.94          0.00
> ATOM    162  CG2 VAL X  23      43.799  25.752  37.471 17     1 1.94          0.00
> ATOM    163  C   VAL X  23      41.160  26.108  40.238  3     0 1.67          0.60
> ATOM    164  O   VAL X  23      41.223  25.719  41.402  4     1 1.38         -0.55
> ATOM    165  N   ARG X  24      40.575  27.295  40.088  1     0 1.63         -0.15
> ATOM    166  CA  ARG X  24      39.991  28.021  41.226  2     1 2.03          0.10
> ATOM    167  CB  ARG X  24      40.130  29.516  40.925  6     1 1.99          0.00
> ATOM    168  CG  ARG X  24      41.581  30.000  41.026 16     1 1.99          0.00
> ATOM    169  CD  ARG X  24      41.855  31.412  40.495 12     1 1.99          0.10
> ATOM    170  NE  ARG X  24      43.183  31.871  40.923 12     1 1.63         -0.10
> ATOM    171  CZ  ARG X  24      43.773  33.043  40.677 10     1 1.67          0.50
> ATOM    172  NH1 ARG X  24      43.121  33.998  40.007 10     1 1.63          0.25
> ATOM    173  NH2 ARG X  24      44.966  33.345  41.205 10     1 1.63          0.25
> ATOM    174  C   ARG X  24      38.548  27.657  41.572  3     0 1.67          0.60
> ATOM    175  O   ARG X  24      37.610  28.406  41.316  4     1 1.38         -0.55
> ATOM    176  N   ARG X  25      38.562  26.723  42.527  1     1 1.63         -0.15
> ATOM    177  CA  ARG X  25      37.378  26.059  43.091  2     1 2.03          0.10
> ATOM    178  CB  ARG X  25      37.544  24.532  43.152  6     1 1.99          0.00
> ATOM    179  CG  ARG X  25      38.012  24.067  41.770 16     1 1.99          0.00
> ATOM    180  CD  ARG X  25      38.096  22.545  41.802 12     1 1.99          0.10
> ATOM    181  NE  ARG X  25      38.155  22.021  40.431 12     1 1.63         -0.10
> ATOM    182  CZ  ARG X  25      37.467  20.966  39.970 10     1 1.67          0.50
> ATOM    183  NH1 ARG X  25      36.800  20.194  40.849 10     1 1.63          0.25
> ATOM    184  NH2 ARG X  25      38.063  20.409  38.903 10     1 1.63          0.25
> ATOM    185  C   ARG X  25      36.719  26.541  44.389  3     0 1.67          0.60
> ATOM    186  O   ARG X  25      37.186  26.270  45.496  4     1 1.38         -0.55
> ATOM    187  N   PHE X  26      35.479  26.968  44.154  1     0 1.63         -0.15
> ATOM    188  CA  PHE X  26      34.561  27.520  45.152  2     1 2.03          0.10
> ATOM    189  CB  PHE X  26      34.311  28.991  44.804  6     1 1.99          0.00
> ATOM    190  CG  PHE X  26      35.582  29.849  44.839 16     1 1.82          0.00
> ATOM    191  CD1 PHE X  26      36.252  30.235  43.688 16     1 1.78          0.00
> ATOM    192  CD2 PHE X  26      36.214  30.009  46.069 16     1 1.78          0.00
> ATOM    193  CE1 PHE X  26      37.482  30.859  43.804 16     1 1.78          0.00
> ATOM    194  CE2 PHE X  26      37.485  30.557  46.196 16     1 1.78          0.00
> ATOM    195  CZ  PHE X  26      38.112  31.013  45.041 16     1 1.78          0.00
> ATOM    196  C   PHE X  26      33.249  26.789  45.437  3     1 1.67          0.60
> ATOM    197  O   PHE X  26      32.493  27.361  46.221  4     1 1.38         -0.55
> ATOM    198  N   PHE X  27      33.309  25.482  45.219  1     0 1.63         -0.15
> ATOM    199  CA  PHE X  27      32.044  24.729  45.292  2     1 2.03          0.10
> ATOM    200  CB  PHE X  27      31.441  24.438  43.913  6     1 1.99          0.00
> ATOM    201  CG  PHE X  27      30.900  25.781  43.423 16     1 1.82          0.00
> ATOM    202  CD1 PHE X  27      31.634  26.293  42.357 16     1 1.78          0.00
> ATOM    203  CD2 PHE X  27      29.825  26.505  43.911 16     1 1.78          0.00
> ATOM    204  CE1 PHE X  27      31.224  27.463  41.733 16     1 1.78          0.00
> ATOM    205  CE2 PHE X  27      29.450  27.689  43.293 16     1 1.78          0.00
> ATOM    206  CZ  PHE X  27      30.101  28.160  42.159 16     1 1.78          0.00
> ATOM    207  C   PHE X  27      32.162  23.399  46.031  3     1 1.67          0.60
> ATOM    208  O   PHE X  27      31.847  22.344  45.470  4     1 1.38         -0.55
> ATOM    209  N   LYS X  28      32.391  23.602  47.323  1     1 1.63         -0.15
> ATOM    210  CA  LYS X  28      32.531  22.558  48.346  2     1 2.03          0.10
> ATOM    211  CB  LYS X  28      33.723  22.870  49.262  6     1 1.99          0.00
> ATOM    212  CG  LYS X  28      35.055  22.915  48.513 16     1 1.99          0.00
> ATOM    213  CD  LYS X  28      36.134  23.081  49.585  8     1 1.99          0.00
> ATOM    214  CE  LYS X  28      37.430  23.185  48.783  7     1 1.99          0.25
> ATOM    215  NZ  LYS X  28      38.628  23.554  49.534  7     1 1.47          0.75
> ATOM    216  C   LYS X  28      31.248  22.347  49.138  3     1 1.67          0.60
> ATOM    217  O   LYS X  28      30.828  23.134  49.989  4     1 1.38         -0.55
> ATOM    218  N   SER X  29      30.481  21.460  48.508  1     1 1.63         -0.15
> ATOM    219  CA  SER X  29      29.249  20.804  48.973  2     1 2.03          0.10
> ATOM    220  CB  SER X  29      28.078  21.775  49.033 13     1 1.99          0.25
> ATOM    221  OG  SER X  29      27.954  22.680  47.931 13     1 1.38         -0.25
> ATOM    222  C   SER X  29      28.893  19.510  48.232  3     1 1.67          0.60
> ATOM    223  O1  SER X  29      29.552  19.151  47.234  0     1 1.90          0.00
> ATOM    224  O2  SER X  29      27.914  18.951  48.763  0     1 1.90          0.00
>
>
> ______________________________________________________________________
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