[gmx-users] a strange behavior in editconf -rotate

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jun 23 08:19:14 CEST 2006


Hi Dongsheng Zhang,

Rotating the system with editconf does not change the box. It is
likely that you rotated your molecule with respect to the box, such
that you have caused severe overlaps. Glancing at your coordinates
(notably z) and the box vectors supports this. Try creating a new box
for the rotated molecule.

Cheers,

Tsjerk

On 6/22/06, Dongsheng Zhang <dong at pampas.chem.purdue.edu> wrote:
> Dear GMX users,
>
>
> I have generated a pdb file (test1.pdb) for a PPO chain. I can do energy
> minimization for this chain using oplsaa FF. However, if I rotate the
> chain by
> editconf -f test1.pdb -rotate 9 -9 0 -o test2.pdb
>
> then I can't do EM for test2.pdb. Could anyone tell me why the rotation
> of a molecule can affect EM? Thank you in advance!
>
>
> If you want to test my case, please add PPO to aminoacids.dat, and [PPO]
> building block to ffoplsaa.rtp
>
> By the way, is it possible to add one more function of genconf to extend
> a chain by translation?
>
> The detailed information is as follows:
>
> test1.pdb
>
> TITLE     15PPO.pdb
> REMARK    THIS IS A SIMULATION BOX
> CRYST1   19.900   12.630   11.640  90.00  90.00  90.00 P 1           1
> MODEL        1
> ATOM      1  CH3 PPO     1      -8.740   0.260 -77.460  1.00  0.00
> ATOM      2 HH31 PPO     1      -8.400  -0.180 -76.540  1.00  0.00
> ATOM      3 HH32 PPO     1      -7.990   0.040 -78.190  1.00  0.00
> ATOM      4 HH33 PPO     1      -8.800   1.330 -77.320  1.00  0.00
> ATOM      5  CH  PPO     1     -10.000  -0.360 -77.990  1.00  0.00
> ATOM      6  HH  PPO     1      -9.960  -1.430 -77.960  1.00  0.00
> ATOM      7  CH2 PPO     1     -10.150   0.020 -79.440  1.00  0.00
> ATOM      8 HH21 PPO     1     -10.610   0.990 -79.570  1.00  0.00
> ATOM      9 HH22 PPO     1      -9.140   0.110 -79.800  1.00  0.00
> ATOM     10  O   PPO     1     -10.740  -1.000 -80.240  1.00  0.00
> ATOM     11  CH3 PPO     2     -10.550  -3.410 -80.440  1.00  0.00
> ATOM     12 HH31 PPO     2     -11.510  -3.460 -80.940  1.00  0.00
> ATOM     13 HH32 PPO     2     -10.710  -3.610 -79.380  1.00  0.00
> ATOM     14 HH33 PPO     2      -9.980  -4.250 -80.790  1.00  0.00
> ATOM     15  CH  PPO     2      -9.850  -2.050 -80.630  1.00  0.00
> ATOM     16  HH  PPO     2      -9.180  -2.070 -79.800  1.00  0.00
> ATOM     17  CH2 PPO     2      -8.670  -1.940 -81.680  1.00  0.00
> ATOM     18 HH21 PPO     2      -8.620  -2.970 -81.800  1.00  0.00
> ATOM     19 HH22 PPO     2      -7.800  -1.670 -81.100  1.00  0.00
> ATOM     20  O   PPO     2      -8.540  -1.320 -83.030  1.00  0.00
> ATOM     21  CH3 PPO     3      -8.300  -3.490 -84.140  1.00  0.00
> ATOM     22 HH31 PPO     3      -7.310  -3.850 -84.160  1.00  0.00
> ATOM     23 HH32 PPO     3      -8.960  -3.880 -84.890  1.00  0.00
> ATOM     24 HH33 PPO     3      -8.670  -4.020 -83.290  1.00  0.00
> ATOM     25  CH  PPO     3      -8.200  -1.980 -84.280  1.00  0.00
> ATOM     26  HH  PPO     3      -7.240  -1.550 -84.240  1.00  0.00
> ATOM     27  CH2 PPO     3      -7.980  -1.490 -85.770  1.00  0.00
> ATOM     28 HH21 PPO     3      -8.230  -0.480 -85.940  1.00  0.00
> ATOM     29 HH22 PPO     3      -6.950  -1.520 -86.120  1.00  0.00
> ATOM     30  O   PPO     3      -8.620  -2.430 -86.580  1.00  0.00
> ATOM     31  CH3 PPO     4      -9.510  -3.830 -87.970  1.00  0.00
> ATOM     32 HH31 PPO     4     -10.320  -3.720 -88.690  1.00  0.00
> ATOM     33 HH32 PPO     4      -9.890  -4.010 -86.980  1.00  0.00
> ATOM     34 HH33 PPO     4      -8.960  -4.710 -88.190  1.00  0.00
> ATOM     35  CH  PPO     4      -8.580  -2.670 -88.000  1.00  0.00
> ATOM     36  HH  PPO     4      -7.570  -2.820 -87.700  1.00  0.00
> ATOM     37  CH2 PPO     4      -7.740  -2.850 -89.270  1.00  0.00
> ATOM     38 HH21 PPO     4      -7.150  -1.990 -89.580  1.00  0.00
> ATOM     39 HH22 PPO     4      -8.470  -3.050 -90.020  1.00  0.00
> ATOM     40  O   PPO     4      -7.080  -4.090 -89.380  1.00  0.00
> ATOM     41  CH3 PPO     5      -5.570  -5.590 -90.290  1.00  0.00
> ATOM     42 HH31 PPO     5      -5.430  -6.280 -91.110  1.00  0.00
> ATOM     43 HH32 PPO     5      -5.850  -6.150 -89.440  1.00  0.00
> ATOM     44 HH33 PPO     5      -4.550  -5.380 -90.170  1.00  0.00
> ATOM     45  CH  PPO     5      -6.280  -4.220 -90.540  1.00  0.00
> ATOM     46  HH  PPO     5      -5.670  -3.390 -90.260  1.00  0.00
> ATOM     47  CH2 PPO     5      -6.900  -4.060 -92.030  1.00  0.00
> ATOM     48 HH21 PPO     5      -7.960  -4.120 -91.940  1.00  0.00
> ATOM     49 HH22 PPO     5      -6.770  -5.070 -92.320  1.00  0.00
> ATOM     50  O   PPO     5      -6.510  -3.440 -93.380  1.00  0.00
> ATOM     51  CH3 PPO     6      -5.210  -1.190 -93.590  1.00  0.00
> ATOM     52 HH31 PPO     6      -4.210  -1.160 -93.270  1.00  0.00
> ATOM     53 HH32 PPO     6      -5.790  -1.000 -92.710  1.00  0.00
> ATOM     54 HH33 PPO     6      -5.300  -0.320 -94.220  1.00  0.00
> ATOM     55  CH  PPO     6      -5.540  -2.590 -94.170  1.00  0.00
> ATOM     56  HH  PPO     6      -6.380  -2.030 -94.370  1.00  0.00
> ATOM     57  CH2 PPO     6      -5.030  -2.910 -95.730  1.00  0.00
> ATOM     58 HH21 PPO     6      -5.630  -2.520 -96.520  1.00  0.00
> ATOM     59 HH22 PPO     6      -4.290  -2.120 -95.780  1.00  0.00
> ATOM     60  O   PPO     6      -4.050  -3.870 -96.340  1.00  0.00
> ATOM     61  CH3 PPO     7      -4.000  -6.800 -96.280  1.00  0.00
> ATOM     62 HH31 PPO     7      -3.560  -6.990 -95.330  1.00  0.00
> ATOM     63 HH32 PPO     7      -3.540  -7.460 -97.010  1.00  0.00
> ATOM     64 HH33 PPO     7      -4.840  -7.450 -96.190  1.00  0.00
> ATOM     65  CH  PPO     7      -3.970  -5.270 -96.880  1.00  0.00
> ATOM     66  HH  PPO     7      -2.930  -5.010 -96.850  1.00  0.00
> ATOM     67  CH2 PPO     7      -4.000  -5.390 -98.350  1.00  0.00
> ATOM     68 HH21 PPO     7      -4.530  -6.200 -98.810  1.00  0.00
> ATOM     69 HH22 PPO     7      -3.050  -5.680 -98.650  1.00  0.00
> ATOM     70  O   PPO     7      -4.390  -4.120 -98.750  1.00  0.00
> ATOM     71  CH3 PPO     8      -3.830  -1.930 -98.750  1.00  0.00
> ATOM     72 HH31 PPO     8      -4.910  -1.910 -98.890  1.00  0.00
> ATOM     73 HH32 PPO     8      -3.620  -1.600 -97.740  1.00  0.00
> ATOM     74 HH33 PPO     8      -3.340  -1.200 -99.380  1.00  0.00
> ATOM     75  CH  PPO     8      -3.300  -3.330 -98.990  1.00  0.00
> ATOM     76  HH  PPO     8      -2.430  -3.500 -98.350  1.00  0.00
> ATOM     77  CH2 PPO     8      -3.040  -3.840-100.380  1.00  0.00
> ATOM     78 HH21 PPO     8      -3.230  -4.890-100.490  1.00  0.00
> ATOM     79 HH22 PPO     8      -1.990  -3.810-100.630  1.00  0.00
> ATOM     80  O   PPO     8      -3.960  -3.250-101.230  1.00  0.00
> ATOM     81  CH3 PPO     9      -3.490  -1.510-102.400  1.00  0.00
> ATOM     82 HH31 PPO     9      -3.420  -1.140-101.420  1.00  0.00
> ATOM     83 HH32 PPO     9      -4.390  -1.060-102.790  1.00  0.00
> ATOM     84 HH33 PPO     9      -2.670  -1.190-102.990  1.00  0.00
> ATOM     85  CH  PPO     9      -3.340  -2.980-102.430  1.00  0.00
> ATOM     86  HH  PPO     9      -2.280  -3.220-102.510  1.00  0.00
> ATOM     87  CH2 PPO     9      -4.050  -3.420-103.650  1.00  0.00
> ATOM     88 HH21 PPO     9      -4.910  -2.830-103.600  1.00  0.00
> ATOM     89 HH22 PPO     9      -3.430  -2.890-104.310  1.00  0.00
> ATOM     90  O   PPO     9      -4.400  -4.810-104.010  1.00  0.00
> ATOM     91  CH3 PPO    10      -3.390  -4.700-105.770  1.00  0.00
> ATOM     92 HH31 PPO    10      -3.370  -3.670-106.020  1.00  0.00
> ATOM     93 HH32 PPO    10      -2.900  -5.190-106.520  1.00  0.00
> ATOM     94 HH33 PPO    10      -2.660  -4.590-105.040  1.00  0.00
> ATOM     95  CH  PPO    10      -4.630  -5.400-105.360  1.00  0.00
> ATOM     96  HH  PPO    10      -4.310  -6.410-105.110  1.00  0.00
> ATOM     97  CH2 PPO    10      -6.030  -5.600-106.320  1.00  0.00
> ATOM     98 HH21 PPO    10      -6.980  -5.320-105.910  1.00  0.00
> ATOM     99 HH22 PPO    10      -6.050  -6.620-105.970  1.00  0.00
> ATOM    100  O   PPO    10      -6.550  -6.320-107.550  1.00  0.00
> ATOM    101  CH3 PPO    11      -6.820  -4.690-109.670  1.00  0.00
> ATOM    102 HH31 PPO    11      -6.700  -3.660-109.440  1.00  0.00
> ATOM    103 HH32 PPO    11      -6.150  -4.450-108.890  1.00  0.00
> ATOM    104 HH33 PPO    11      -7.880  -4.620-109.610  1.00  0.00
> ATOM    105  CH  PPO    11      -6.830  -6.020-108.990  1.00  0.00
> ATOM    106  HH  PPO    11      -5.900  -6.390-109.120  1.00  0.00
> ATOM    107  CH2 PPO    11      -7.130  -6.970-110.190  1.00  0.00
> ATOM    108 HH21 PPO    11      -6.470  -6.580-110.950  1.00  0.00
> ATOM    109 HH22 PPO    11      -6.760  -7.980-110.070  1.00  0.00
> ATOM    110  O   PPO    11      -8.380  -6.790-110.850  1.00  0.00
> ATOM    111  CH3 PPO    12      -9.250  -8.530-112.070  1.00  0.00
> ATOM    112 HH31 PPO    12      -9.220  -9.140-112.980  1.00  0.00
> ATOM    113 HH32 PPO    12     -10.280  -8.240-111.920  1.00  0.00
> ATOM    114 HH33 PPO    12      -8.890  -9.120-111.230  1.00  0.00
> ATOM    115  CH  PPO    12      -8.420  -7.290-112.210  1.00  0.00
> ATOM    116  HH  PPO    12      -7.430  -7.580-112.570  1.00  0.00
> ATOM    117  CH2 PPO    12      -9.100  -6.370-113.280  1.00  0.00
> ATOM    118 HH21 PPO    12      -8.440  -5.630-113.680  1.00  0.00
> ATOM    119 HH22 PPO    12      -9.920  -5.810-112.890  1.00  0.00
> ATOM    120  O   PPO    12      -9.720  -7.110-114.310  1.00  0.00
> ATOM    121  CH3 PPO    13      -7.660  -7.600-115.360  1.00  0.00
> ATOM    122 HH31 PPO    13      -7.080  -7.580-116.260  1.00  0.00
> ATOM    123 HH32 PPO    13      -7.620  -8.520-114.840  1.00  0.00
> ATOM    124 HH33 PPO    13      -7.190  -6.910-114.730  1.00  0.00
> ATOM    125  CH  PPO    13      -9.060  -7.140-115.560  1.00  0.00
> ATOM    126  HH  PPO    13      -8.910  -6.140-115.950  1.00  0.00
> ATOM    127  CH2 PPO    13      -9.860  -8.050-116.520  1.00  0.00
> ATOM    128 HH21 PPO    13      -9.210  -8.600-117.200  1.00  0.00
> ATOM    129 HH22 PPO    13     -10.320  -8.860-115.940  1.00  0.00
> ATOM    130  O   PPO    13     -10.870  -7.310-117.220  1.00  0.00
> ATOM    131  CH3 PPO    14      -9.190  -6.730-118.850  1.00  0.00
> ATOM    132 HH31 PPO    14      -9.260  -7.650-119.420  1.00  0.00
> ATOM    133 HH32 PPO    14      -8.380  -6.930-118.180  1.00  0.00
> ATOM    134 HH33 PPO    14      -8.910  -5.940-119.520  1.00  0.00
> ATOM    135  CH  PPO    14     -10.390  -6.260-118.060  1.00  0.00
> ATOM    136  HH  PPO    14     -10.000  -5.480-117.430  1.00  0.00
> ATOM    137  CH2 PPO    14     -11.420  -5.390-118.820  1.00  0.00
> ATOM    138 HH21 PPO    14     -10.950  -4.490-119.230  1.00  0.00
> ATOM    139 HH22 PPO    14     -12.150  -5.010-118.110  1.00  0.00
> ATOM    140  O   PPO    14     -12.140  -6.000-119.870  1.00  0.00
> ATOM    141  CH3 PPO    15     -11.080  -7.740-121.000  1.00  0.00
> ATOM    142 HH31 PPO    15     -10.090  -8.000-121.340  1.00  0.00
> ATOM    143 HH32 PPO    15     -11.690  -8.310-121.650  1.00  0.00
> ATOM    144 HH33 PPO    15     -11.210  -8.160-120.000  1.00  0.00
> ATOM    145  CH  PPO    15     -11.360  -6.240-121.030  1.00  0.00
> ATOM    146  HH  PPO    15     -10.360  -5.830-120.960  1.00  0.00
> ATOM    147  CH2 PPO    15     -11.920  -5.560-122.300  1.00  0.00
> ATOM    148 HH21 PPO    15     -11.450  -5.950-123.200  1.00  0.00
> ATOM    149 HH22 PPO    15     -11.730  -4.510-122.210  1.00  0.00
> ATOM    150  O   PPO    15     -13.300  -5.320-122.460  1.00  0.00
> TER
> ENDMDL
>
>
> test2.pdb:
>
> TITLE     15PPO.pdb
> REMARK    THIS IS A SIMULATION BOX
> CRYST1   19.900   12.630   11.640  90.00  90.00  90.00 P 1           1
> MODEL        1
> ATOM      1  CH3 PPO     1       3.329  12.374 -76.891  1.00  0.00
> ATOM      2 HH31 PPO     1       3.534  11.796 -76.009  1.00  0.00
> ATOM      3 HH32 PPO     1       4.188  12.271 -77.520  1.00  0.00
> ATOM      4 HH33 PPO     1       3.222  13.409 -76.599  1.00  0.00
> ATOM      5  CH  PPO     1       2.182  11.845 -77.701  1.00  0.00
> ATOM      6  HH  PPO     1       2.243  10.783 -77.831  1.00  0.00
> ATOM      7  CH2 PPO     1       2.249  12.447 -79.081  1.00  0.00
> ATOM      8 HH21 PPO     1       1.791  13.425 -79.130  1.00  0.00
> ATOM      9 HH22 PPO     1       3.300  12.592 -79.260  1.00  0.00
> ATOM     10  O   PPO     1       1.814  11.565 -80.111  1.00  0.00
> ATOM     11  CH3 PPO     2       2.092   9.216 -80.649  1.00  0.00
> ATOM     12 HH31 PPO     2       1.222   9.244 -81.294  1.00  0.00
> ATOM     13 HH32 PPO     2       1.775   8.852 -79.671  1.00  0.00
> ATOM     14 HH33 PPO     2       2.730   8.441 -81.031  1.00  0.00
> ATOM     15  CH  PPO     2       2.779  10.589 -80.514  1.00  0.00
> ATOM     16  HH  PPO     2       3.313  10.439 -79.603  1.00  0.00
> ATOM     17  CH2 PPO     2       4.104  10.861 -81.337  1.00  0.00
> ATOM     18 HH21 PPO     2       4.198   9.863 -81.606  1.00  0.00
> ATOM     19 HH22 PPO     2       4.868  11.037 -80.594  1.00  0.00
> ATOM     20  O   PPO     2       4.426  11.685 -82.538  1.00  0.00
> ATOM     21  CH3 PPO     3       4.888   9.715 -83.919  1.00  0.00
> ATOM     22 HH31 PPO     3       5.878   9.363 -83.839  1.00  0.00
> ATOM     23 HH32 PPO     3       4.361   9.447 -84.814  1.00  0.00
> ATOM     24 HH33 PPO     3       4.404   9.059 -83.229  1.00  0.00
> ATOM     25  CH  PPO     3       4.971  11.229 -83.806  1.00  0.00
> ATOM     26  HH  PPO     3       5.903  11.647 -83.551  1.00  0.00
> ATOM     27  CH2 PPO     3       5.407  11.946 -85.150  1.00  0.00
> ATOM     28 HH21 PPO     3       5.162  12.970 -85.199  1.00  0.00
> ATOM     29 HH22 PPO     3       6.479  11.971 -85.335  1.00  0.00
> ATOM     30  O   PPO     3       4.923  11.144 -86.185  1.00  0.00
> ATOM     31  CH3 PPO     4       4.293   9.979 -87.897  1.00  0.00
> ATOM     32 HH31 PPO     4       3.601  10.200 -88.709  1.00  0.00
> ATOM     33 HH32 PPO     4       3.769   9.646 -87.018  1.00  0.00
> ATOM     34 HH33 PPO     4       4.892   9.144 -88.161  1.00  0.00
> ATOM     35  CH  PPO     4       5.188  11.129 -87.601  1.00  0.00
> ATOM     36  HH  PPO     4       6.143  10.934 -87.174  1.00  0.00
> ATOM     37  CH2 PPO     4       6.218  11.150 -88.737  1.00  0.00
> ATOM     38 HH21 PPO     4       6.828  12.048 -88.814  1.00  0.00
> ATOM     39 HH22 PPO     4       5.618  11.070 -89.613  1.00  0.00
> ATOM     40  O   PPO     4       6.917   9.942 -88.932  1.00  0.00
> ATOM     41  CH3 PPO     5       8.586   8.603 -89.815  1.00  0.00
> ATOM     42 HH31 PPO     5       8.868   8.050 -90.700  1.00  0.00
> ATOM     43 HH32 PPO     5       8.192   7.917 -89.117  1.00  0.00
> ATOM     44 HH33 PPO     5       9.570   8.792 -89.506  1.00  0.00
> ATOM     45  CH  PPO     5       7.890   9.996 -89.959  1.00  0.00
> ATOM     46  HH  PPO     5       8.429  10.772 -89.462  1.00  0.00
> ATOM     47  CH2 PPO     5       7.504  10.387 -91.485  1.00  0.00
> ATOM     48 HH21 PPO     5       6.444  10.313 -91.572  1.00  0.00
> ATOM     49 HH22 PPO     5       7.702   9.434 -91.903  1.00  0.00
> ATOM     50  O   PPO     5       8.082  11.210 -92.645  1.00  0.00
> ATOM     51  CH3 PPO     6       9.344  13.465 -92.299  1.00  0.00
> ATOM     52 HH31 PPO     6      10.281  13.445 -91.825  1.00  0.00
> ATOM     53 HH32 PPO     6       8.630  13.515 -91.501  1.00  0.00
> ATOM     54 HH33 PPO     6       9.331  14.423 -92.793  1.00  0.00
> ATOM     55  CH  PPO     6       9.142  12.173 -93.132  1.00  0.00
> ATOM     56  HH  PPO     6       8.329  12.758 -93.372  1.00  0.00
> ATOM     57  CH2 PPO     6       9.894  12.101 -94.624  1.00  0.00
> ATOM     58 HH21 PPO     6       9.414  12.610 -95.428  1.00  0.00
> ATOM     59 HH22 PPO     6      10.614  12.889 -94.435  1.00  0.00
> ATOM     60  O   PPO     6      10.980  11.249 -95.214  1.00  0.00
> ATOM     61  CH3 PPO     7      11.092   8.345 -95.600  1.00  0.00
> ATOM     62 HH31 PPO     7      11.384   8.009 -94.634  1.00  0.00
> ATOM     63 HH32 PPO     7      11.675   7.808 -96.342  1.00  0.00
> ATOM     64 HH33 PPO     7      10.264   7.689 -95.744  1.00  0.00
> ATOM     65  CH  PPO     7      11.177   9.950 -95.944  1.00  0.00
> ATOM     66  HH  PPO     7      12.193  10.202 -95.712  1.00  0.00
> ATOM     67  CH2 PPO     7      11.377  10.062 -97.402  1.00  0.00
> ATOM     68 HH21 PPO     7      10.944   9.334 -98.059  1.00  0.00
> ATOM     69 HH22 PPO     7      12.369   9.822 -97.591  1.00  0.00
> ATOM     70  O   PPO     7      11.023  11.379 -97.657  1.00  0.00
> ATOM     71  CH3 PPO     8      11.522  13.542 -97.231  1.00  0.00
> ATOM     72 HH31 PPO     8      10.477  13.583 -97.533  1.00  0.00
> ATOM     73 HH32 PPO     8      11.565  13.710 -96.162  1.00  0.00
> ATOM     74 HH33 PPO     8      12.086  14.361 -97.656  1.00  0.00
> ATOM     75  CH  PPO     8      12.117  12.196 -97.598  1.00  0.00
> ATOM     76  HH  PPO     8      12.881  11.928 -96.864  1.00  0.00
> ATOM     77  CH2 PPO     8      12.601  11.910 -98.992  1.00  0.00
> ATOM     78 HH21 PPO     8      12.456  10.890 -99.292  1.00  0.00
> ATOM     79 HH22 PPO     8      13.676  11.979 -99.067  1.00  0.00
> ATOM     80  O   PPO     8      11.809  12.626 -99.874  1.00  0.00
> ATOM     81  CH3 PPO     9      12.412  14.527-100.673  1.00  0.00
> ATOM     82 HH31 PPO     9      12.320  14.740 -99.649  1.00  0.00
> ATOM     83 HH32 PPO     9      11.572  15.033-101.125  1.00  0.00
> ATOM     84 HH33 PPO     9      13.305  14.936-101.071  1.00  0.00
> ATOM     85  CH  PPO     9      12.600  13.080-100.906  1.00  0.00
> ATOM     86  HH  PPO     9      13.666  12.856-100.856  1.00  0.00
> ATOM     87  CH2 PPO     9      12.098  12.837-102.275  1.00  0.00
> ATOM     88 HH21 PPO     9      11.227  13.411-102.270  1.00  0.00
> ATOM     89 HH22 PPO     9      12.800  13.463-102.740  1.00  0.00
> ATOM     90  O   PPO     9      11.842  11.520-102.896  1.00  0.00
> ATOM     91  CH3 PPO    10      13.109  11.904-104.438  1.00  0.00
> ATOM     92 HH31 PPO    10      13.142  12.960-104.520  1.00  0.00
> ATOM     93 HH32 PPO    10      13.721  11.537-105.169  1.00  0.00
> ATOM     94 HH33 PPO    10      13.715  11.898-103.595  1.00  0.00
> ATOM     95  CH  PPO    10      11.838  11.148-104.340  1.00  0.00
> ATOM     96  HH  PPO    10      12.140  10.112-104.202  1.00  0.00
> ATOM     97  CH2 PPO    10      10.609  11.101-105.527  1.00  0.00
> ATOM     98 HH21 PPO    10       9.600  11.313-105.232  1.00  0.00
> ATOM     99 HH22 PPO    10      10.560  10.039-105.346  1.00  0.00
> ATOM    100  O   PPO    10      10.303  10.582-106.919  1.00  0.00
> ATOM    101  CH3 PPO    11      10.324  12.524-108.778  1.00  0.00
> ATOM    102 HH31 PPO    11      10.381  13.505-108.375  1.00  0.00
> ATOM    103 HH32 PPO    11      10.859  12.639-107.875  1.00  0.00
> ATOM    104 HH33 PPO    11       9.266  12.584-108.874  1.00  0.00
> ATOM    105  CH  PPO    11      10.241  11.104-108.321  1.00  0.00
> ATOM    106  HH  PPO    11      11.189  10.759-108.360  1.00  0.00
> ATOM    107  CH2 PPO    11      10.154  10.353-109.686  1.00  0.00
> ATOM    108 HH21 PPO    11      10.913  10.857-110.264  1.00  0.00
> ATOM    109 HH22 PPO    11      10.525   9.337-109.667  1.00  0.00
> ATOM    110  O   PPO    11       9.017  10.634-110.497  1.00  0.00
> ATOM    111  CH3 PPO    12       8.388   9.107-112.092  1.00  0.00
> ATOM    112 HH31 PPO    12       8.574   8.646-113.070  1.00  0.00
> ATOM    113 HH32 PPO    12       7.341   9.370-112.062  1.00  0.00
> ATOM    114 HH33 PPO    12       8.629   8.392-111.308  1.00  0.00
> ATOM    115  CH  PPO    12       9.199  10.353-111.908  1.00  0.00
> ATOM    116  HH  PPO    12      10.240  10.123-112.149  1.00  0.00
> ATOM    117  CH2 PPO    12       8.671  11.429-112.916  1.00  0.00
> ATOM    118 HH21 PPO    12       9.366  12.223-113.088  1.00  0.00
> ATOM    119 HH22 PPO    12       7.787  11.921-112.577  1.00  0.00
> ATOM    120  O   PPO    12       8.236  10.860-114.132  1.00  0.00
> ATOM    121  CH3 PPO    13      10.444  10.540-114.909  1.00  0.00
> ATOM    122 HH31 PPO    13      11.156  10.700-115.694  1.00  0.00
> ATOM    123 HH32 PPO    13      10.426   9.550-114.538  1.00  0.00
> ATOM    124 HH33 PPO    13      10.794  11.123-114.115  1.00  0.00
> ATOM    125  CH  PPO    13       9.081  11.025-115.253  1.00  0.00
> ATOM    126  HH  PPO    13       9.265  12.074-115.455  1.00  0.00
> ATOM    127  CH2 PPO    13       8.462  10.277-116.455  1.00  0.00
> ATOM    128 HH21 PPO    13       9.222   9.840-117.101  1.00  0.00
> ATOM    129 HH22 PPO    13       7.938   9.386-116.086  1.00  0.00
> ATOM    130  O   PPO    13       7.554  11.117-117.181  1.00  0.00
> ATOM    131  CH3 PPO    14       9.451  11.945-118.419  1.00  0.00
> ATOM    132 HH31 PPO    14       9.493  11.126-119.128  1.00  0.00
> ATOM    133 HH32 PPO    14      10.153  11.643-117.670  1.00  0.00
> ATOM    134 HH33 PPO    14       9.812  12.830-118.907  1.00  0.00
> ATOM    135  CH  PPO    14       8.132  12.286-117.763  1.00  0.00
> ATOM    136  HH  PPO    14       8.401  12.958-116.967  1.00  0.00
> ATOM    137  CH2 PPO    14       7.211  13.264-118.532  1.00  0.00
> ATOM    138 HH21 PPO    14       7.717  14.217-118.719  1.00  0.00
> ATOM    139 HH22 PPO    14       6.371  13.528-117.894  1.00  0.00
> ATOM    140  O   PPO    14       6.677  12.826-119.763  1.00  0.00
> ATOM    141  CH3 PPO    15       7.941  11.284-120.968  1.00  0.00
> ATOM    142 HH31 PPO    15       8.978  11.080-121.185  1.00  0.00
> ATOM    143 HH32 PPO    15       7.453  10.823-121.786  1.00  0.00
> ATOM    144 HH33 PPO    15       7.669  10.713-120.078  1.00  0.00
> ATOM    145  CH  PPO    15       7.633  12.770-120.809  1.00  0.00
> ATOM    146  HH  PPO    15       8.600  13.164-120.521  1.00  0.00
> ATOM    147  CH2 PPO    15       7.259  13.640-122.031  1.00  0.00
> ATOM    148 HH21 PPO    15       7.872  13.396-122.896  1.00  0.00
> ATOM    149 HH22 PPO    15       7.407  14.663-121.751  1.00  0.00
> ATOM    150  O   PPO    15       5.915  13.902-122.366  1.00  0.00
> TER
> ENDMDL
>
>
> add the following to ffoplsaa.rtp
> [ PPO ]
>  [ atoms ]
>    CH3    opls_135   -0.180     1
>   HH31    opls_140    0.060     1
>   HH32    opls_140    0.060     1
>   HH33    opls_140    0.060     1
>     CH    opls_183    0.170     2
>     HH    opls_140    0.060     2
>    CH2    opls_182    0.140     2
>   HH21    opls_140    0.060     2
>   HH22    opls_140    0.060     2
>      O    opls_180   -0.490     2
>  [ bonds ]
>    CH3  HH31
>    CH3  HH32
>    CH3  HH33
>    CH3    CH
>     CH    HH
>     CH    -O
>     CH   CH2
>    CH2  HH21
>    CH2  HH22
>    CH2     O
>
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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336



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