[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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