AMBER Archive (2002)

Subject: Cholesterol PREP file

From: samantha hughes (s.j.hughes_at_ic.ac.uk)
Date: Wed Feb 27 2002 - 09:28:46 CST

Hi All,

I know that PREP is no longer supported, but figure that there are bound
to be people on the list who can help me with this. Does anyone have a
PREP file for cholesterol that they could give me or alternatively tell
me where I am going wrong in my attempts ? I am really struggling to
create a PREP input file for cholesterol that works properly. I have the
crystal structure coordinates, and am using the CHANGE option to read
these in (rather than laboriously figuring out the internal
coordinates). The file runs through PREP properly, but causes a
segmentation fault in LINK. If I load the AMBER PREP file into xLeap,
all of the atoms are at the same point in space (despite the PREP output
report being sensible). I'm including the file to see if anyone can
point out where I am going wrong.I can't find any examples of using the
CHANGE option in the amber5 demo directory.

I know that I could use LEaP, but have good reason for using the PLEP
method instead.

Thanks for any help,
Samantha

>>------------------------------------------------
0 0 2

Cholesterol
cho.res
 CHO INT 0
 CHANGE OMIT DU BEG
   0.0
   1 DUMM DU M 0.000 00.000 0.000
   2 DUMM DU M 0.000 00.000 0.000
   3 DUMM DU M 0.000 00.000 0.000
   4 O1 OH M 3.489 13.841 5.662
   5 H29 HO E 2.608 13.773 6.129
   6 C3 CT M 3.983 12.509 5.362
   7 H34 H1 E 3.329 12.036 4.772
   8 C2 CT M 5.282 12.557 4.672
   9 H32 HC E 5.171 13.065 3.818
  10 H33 HC E 5.938 13.032 5.259
  11 C1 CT M 5.789 11.170 4.371
  12 H30 HC E 6.693 11.230 3.948
  13 H31 HC E 5.158 10.712 3.745
  14 C10 CT M 5.930 10.261 5.621
  15 C19 CT 3 7.059 10.802 6.558
  16 H55 HC E 7.927 10.813 6.062
  17 H56 HC E 7.141 10.209 7.359
  18 H57 HC E 6.832 11.730 6.853
  19 C9 CT M 6.256 8.806 5.169
  20 H41 HC E 5.564 8.708 4.454
  21 C11 CT M 7.635 8.646 4.518
  22 H42 HC E 8.343 8.942 5.159
  23 H43 HC E 7.680 9.205 3.690
  24 C12 CT M 7.990 7.202 4.135
  25 H44 HC E 8.940 7.163 3.825
  26 H45 HC E 7.387 6.894 3.399
  27 C13 CT M 7.818 6.230 5.313
  28 C18 CT 3 8.839 6.546 6.384
  29 H52 HC E 9.760 6.450 6.006
  30 H53 HC E 8.726 5.913 7.150
  31 H54 HC E 8.707 7.484 6.705
  32 C17 CT M 7.779 4.723 4.956
  33 H51 HC E 7.202 4.711 4.140
  34 C20 CT M 9.134 3.952 4.701
  35 H58 HC E 9.656 3.903 5.553
  36 C21 CT 3 9.950 4.638 3.641
  37 H59 HC E 10.793 4.123 3.483
  38 H60 HC E 10.177 5.564 3.942
  39 H61 HC E 9.424 4.684 2.792
  40 C22 CT M 8.835 2.499 4.309
  41 H62 HC E 8.325 2.483 3.449
  42 H63 HC E 8.291 2.065 5.027
  43 C23 CT M 10.067 1.643 4.130
  44 H64 HC E 10.610 1.660 4.970
  45 H65 HC E 10.614 1.999 3.373
  46 C24 CT M 9.657 0.183 3.771
  47 H66 HC E 8.871 0.199 3.153
  48 H67 HC E 9.413 -0.310 4.606
  49 C25 CT M 10.674 -0.750 3.095
  50 H68 HC E 10.875 -0.414 2.175
  51 C26 CT 3 11.736 -0.708 4.028
  52 H69 HC E 12.042 0.237 4.143
  53 H70 HC E 12.496 -1.266 3.694
  54 H71 HC E 11.422 -1.066 4.907
  55 C27 CT M 9.992 -2.164 2.682
  56 H72 HC E 10.650 -2.715 2.169
  57 H73 HC E 9.187 -1.993 2.114
  58 H74 HC E 9.718 -2.656 3.508
  59 C16 CT 3 7.024 4.085 6.126
  60 H49 HC E 6.444 3.354 5.766
  61 H50 HC E 7.628 3.714 6.832
  62 C15 CT 3 6.124 5.210 6.745
  63 H47 HC E 5.156 4.960 6.725
  64 H48 HC E 6.381 5.473 7.675
  65 C14 CT B 6.366 6.380 5.801
  66 H46 HC E 5.828 6.152 4.990
  67 C8 CT B 5.992 7.778 6.284
  68 H40 HC E 6.557 8.023 7.072
  69 C7 CT 3 4.509 7.830 6.681
  70 H38 HC E 3.982 7.351 5.979
  71 H39 HC E 4.405 7.357 7.556
  72 C6 CM B 4.005 9.244 6.810
  73 H37 HC E 3.122 9.339 7.269
  74 C5 CB S 4.636 10.311 6.371
  75 C4 CT B 4.084 11.694 6.666
  76 H35 HC E 3.172 11.578 7.059
  77 H36 HC E 4.668 12.178 7.318

LOOP
C3 C4
C8 C9
C13 C14
C5 C10

DONE
STOP

>>--------------------------------------------

-------------------------------------------------------
Samantha Hughes
Department of Chemistry
Imperial College of Science, Technology and Medicine
Exhibition Road
London
SW7 2AY
-------------------------------------------------------