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

Dongsheng Zhang dong at pampas.chem.purdue.edu
Fri Jun 23 14:37:35 CEST 2006


Dear Tsjerk,

Thank you very much for your reply. You are right. After I specify
pbc=no in mdp file, EM works fine for test2.pdb now.


All the best!


Dongsheng


On Fri, 2006-06-23 at 08:19 +0200, Tsjerk Wassenaar wrote:
> 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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> 
> 



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