From: Dongsheng Zhang (dong_at_pampas.chem.purdue.edu)
Date: Sun Jun 18 2006 - 22:04:53 CDT

Dear VMD users,

I had generate a coordinates file (temp.pdb) for a PPO chain. It is fine
to visualize it by VMD. For my simulation, I need to shift my PPO chain
in y and z directions, so I generate an other coordinates file
(temp2.pdb) by y(new) = y(old) + 15.5, z(new) = z(old) + 20. However,
when I visualize my new PPO chain, I find lots of bond are broken. I
have attached part of my two files, please check them, you can try it.
Does anyone give me a hint what's going on? Thank you in advance!

temp.pdb

ATOM 1 CH3 PPO 1 -2.520 0.230 1.920
ATOM 2 HH31 PPO 1 -2.850 1.210 1.760
ATOM 3 HH32 PPO 1 -3.250 -0.310 2.510
ATOM 4 HH33 PPO 1 -2.600 -0.420 1.020
ATOM 5 CH PPO 1 -1.190 0.200 2.580
ATOM 6 HH PPO 1 -1.170 0.830 3.410
ATOM 7 CH2 PPO 1 -0.900 -1.250 3.020
ATOM 8 HH21 PPO 1 -0.010 -1.260 3.670
ATOM 9 HH22 PPO 1 -1.680 -1.720 3.670
ATOM 10 O PPO 1 -0.750 -2.210 1.990
ATOM 11 CH3 PPO 2 -1.550 -4.260 1.340
ATOM 12 HH31 PPO 2 -2.520 -3.810 1.290
ATOM 13 HH32 PPO 2 -1.790 -5.300 1.540
ATOM 14 HH33 PPO 2 -0.970 -4.050 0.460
ATOM 15 CH PPO 2 -0.720 -3.540 2.390
ATOM 16 HH PPO 2 -1.140 -3.780 3.320
ATOM 17 CH2 PPO 2 0.760 -3.820 2.250
ATOM 18 HH21 PPO 2 1.280 -3.290 1.460
ATOM 19 HH22 PPO 2 1.050 -4.880 2.170
ATOM 20 O PPO 2 1.380 -3.390 3.450
END

temp2.pdb:

ATOM 1 CH PPO 1 -2.520 15.730 21.920
ATOM 2 HH PPO 1 -2.850 16.710 21.760
ATOM 3 CH3 PPO 1 -3.250 15.190 22.510
ATOM 4 HH31 PPO 1 -2.600 15.080 21.020
ATOM 5 HH32 PPO 1 -1.190 15.700 22.580
ATOM 6 HH33 PPO 1 -1.170 16.330 23.410
ATOM 7 CH2 PPO 1 -0.900 14.250 23.020
ATOM 8 HH21 PPO 1 -0.010 14.240 23.670
ATOM 9 HH22 PPO 1 -1.680 13.780 23.670
ATOM 10 O PPO 1 -0.750 13.290 21.990
ATOM 11 CH PPO 2 -1.550 11.240 21.340
ATOM 12 HH PPO 2 -2.520 11.690 21.290
ATOM 13 CH3 PPO 2 -1.790 10.200 21.540
ATOM 14 HH31 PPO 2 -0.970 11.450 20.460
ATOM 15 HH32 PPO 2 -0.720 11.960 22.390
ATOM 16 HH33 PPO 2 -1.140 11.720 23.320
ATOM 17 CH2 PPO 2 0.760 11.680 22.250
ATOM 18 HH21 PPO 2 1.280 12.210 21.460
ATOM 19 HH22 PPO 2 1.050 10.620 22.170
ATOM 20 O PPO 2 1.380 12.110 23.450
END