[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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