From: Crowley, Michael (Michael.Crowley_at_nrel.gov)
Date: Sun Apr 05 2009 - 01:27:03 CDT

 
Dear VMD folks,

I am having much the same trouble as is expressed in the thread:

wrong bonds during loading pdb file(protein plus lipids)

I am running 1.8.6 and 1.8.5 on mac os-x 10.4
Both versions make a mess of carbohydrate pdb's, but not NA or protein.

Below is a pdb that shows the trouble, that being bonds drawn between all atoms.
The very odd thing is that if I load the same pdb 4 times as new molecule, the fourth one and all subsequent ones are fine.

ATOM 2027 C1 NDG A 401 -3.562 15.752 21.491 1.00 39.24
ATOM 2028 C2 NDG A 401 -2.121 16.154 21.042 1.00 37.51
ATOM 2029 C3 NDG A 401 -1.500 17.322 21.901 1.00 32.28
ATOM 2030 C4 NDG A 401 -2.515 18.464 22.046 1.00 34.07
ATOM 2031 C5 NDG A 401 -3.934 17.939 22.444 1.00 38.26
ATOM 2032 C6 NDG A 401 -5.062 18.974 22.487 1.00 41.57
ATOM 2033 C7 NDG A 401 -1.153 14.291 19.650 1.00 34.49
ATOM 2034 C8 NDG A 401 -0.090 13.211 19.579 1.00 30.83
ATOM 2035 O NDG A 401 -4.384 16.919 21.518 1.00 40.77
ATOM 2036 O3 NDG A 401 -0.263 17.836 21.378 1.00 21.01
ATOM 2037 O4 NDG A 401 -2.049 19.432 23.009 1.00 31.26
ATOM 2038 O6 NDG A 401 -5.072 19.956 21.438 1.00 49.57
ATOM 2039 O7 NDG A 401 -1.913 14.458 18.688 1.00 36.13
ATOM 2040 N2 NDG A 401 -1.202 15.034 20.775 1.00 35.82
ATOM 2041 O1L NDG A 401 -3.561 15.338 22.861 1.00 37.20
ATOM 2042 C1 GAL A 402 -2.158 20.795 22.635 1.00 27.02
ATOM 2043 C2 GAL A 402 -1.831 21.633 23.842 1.00 22.59
ATOM 2044 C3 GAL A 402 -1.728 23.122 23.528 1.00 22.91
ATOM 2045 C4 GAL A 402 -0.832 23.359 22.344 1.00 16.49
ATOM 2046 C5 GAL A 402 -1.159 22.398 21.229 1.00 20.72
ATOM 2047 C6 GAL A 402 -0.146 22.366 20.129 1.00 18.92
ATOM 2048 O2 GAL A 402 -2.732 21.366 24.891 1.00 25.35
ATOM 2049 O3 GAL A 402 -1.022 23.679 24.627 1.00 26.25
ATOM 2050 O4 GAL A 402 0.456 22.968 22.807 1.00 19.85
ATOM 2051 O5 GAL A 402 -1.067 21.091 21.782 1.00 26.14
ATOM 2052 O6 GAL A 402 -0.766 21.814 18.971 1.00 29.24

Any help would be appreciated.
Mike