AMBER Archive (2007)

Subject: AMBER: FLAG LENNARD_JONES_ACOEF NAN

From: Greg Gannon (greg.gannon_at_tyndall.ie)
Date: Fri Jul 27 2007 - 09:41:46 CDT

Dear all,
I am a new user of Amber. I wish to generate a prmtop file of a self
assembled monolayer.
Unfortunately my prmtop file (GTS.top) contains NAN in the FLAG
LENNARD_JONES_ACOEF section of the generated file. Below is the
procedure I have be using. Any suggestion as to where the errors lie
will be gratefully received.

The hardware: IBM eServer cluster 1350 consisting of 476 IBM e326
compute nodes with 20 TB of tightly integrated high-performance SAN
based around an IBM DS4500.

Regards
 
Greg

-------------------------------------------------------------
> tleap
---------------------------------------------------------------
> source leap.in

----- Source: ./leap.in
----- Source of ./leap.in done
Loading parameters: ./frcmod.pcy
Reading force field modification type file (frcmod)
Reading title:
frcmod.pcy file
Loading Prep file: ./thiol.in
Loading Prep file: ./gold.in
Loading PDB file: ./firstsamunitwithgold.pdb
  total atoms in file: 194
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 0 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)

----------------------------------------------------------------
CONTENT OF leap.in :

addAtomTypes {
{"A1" "Au" "sp3"}
{"AU" "Au" "sp3"}
{"S" "S" "sp3"}
{"C2" "C" "sp3"}
{"C3" "C" "sp3"}
{"HA" "H" "sp3"}
{"H2" "H" "sp3"}
{"H3" "H" "sp3"}
}
PARM94 = loadamberparams frcmod.pcy
loadAmberPrep thiol.in
loadAmberPrep gold.in
GTS = loadPdb firstsamunitwithgold.pdb
saveAmberParm GTS GTS.top GTS.crd
---------------------------------------------------------------------------------------------------------------------------------
CONTENT OF frcmod.pcy:

MASS
AU 197.
S 32.
C2 12.
C3 12.
HA 1.0
H2 1.0
H3 1.0
A1 197.

BOND
AU-S 198.000 2.531
S-C2 198.000 1.818
C2-HA 309.000 1.111
C2-H2 309.000 1.111
C2-C2 222.500 1.530
C2-C3 222.500 1.528
C3-H3 322.000 1.111

ANGLE
AU-S-C2 0.0 109.00
S-C2-C2 58.000 114.50
S-C2-HA 50.000 109.50
HA-C2-HA 35.500 109.00
C2-C2-C2 58.350 113.60
HA-C2-C2 34.600 110.10
H2-C2-C2 26.500 110.10
H2-C2-H2 35.500 109.00
C2-C2-C3 58.000 115.00
H2-C2-C3 34.600 110.10
H3-C3-C2 34.600 110.10
H3-C3-H3 35.500 108.40

DIHE
AU -S-C2-C2 1 0.00 180.0 2.000
HA -C2-S-AU 1 0.00 0.0 2.000
X -C2-C2-X 1 0.19 0.0 3.000
S -C2-C2-C2 1 0.22 -19.0 2.000
X -C2-C3-X 1 0.16 0.0 3.000

NONB
  AU 1.0370 -0.0780
  S 2.1000 0.4700
  HA 1.3200 -0.0220
  H2 1.3400 0.0320
  H3 1.3200 -0.0230
  C2 2.0100 -0.0600
  C3 2.0200 0.0730
  A1 1.0370 -0.0780

--------------------------------------------------------------------------------------------------------------
CONTENT OF thiol.in:

    1 0 2
C12.dat
C12 dodecane thiol
C12.dat
C12 XYZ 1
CHANGE IOMIT DU ALL
0.0
   1 DUMM DU M 0.000 0.000 0.000 0.00000
   2 DUMM DU M 1.449 0.000 0.000 0.00000
   3 DUMM DU M 1.522 111.100 0.000 0.00000
   4 AU AU M 0.000 0.000 0.000 0.00000
   5 S S M 0.018 -0.179 1.585 -0.07000
   6 CC01 C2 M -0.216 -0.118 3.379 -0.11000
   7 H011 HA E 0.535 0.570 3.823 0.09000
   8 H012 HA E -0.074 -1.135 3.802 0.09000
   9 CC02 C2 M -1.636 0.386 3.704 -0.18000
  10 H021 H2 E -2.389 -0.287 3.241 0.09000
  11 H022 H2 E -1.773 1.411 3.300 0.09000
  12 CC03 C2 M -1.820 0.399 5.233 -0.18000
  13 H031 H2 E -1.058 1.067 5.689 0.09000
  14 H032 H2 E -1.680 -0.629 5.630 0.09000
  15 CC04 C2 M -3.227 0.902 5.606 -0.18000
  16 H041 H2 E -3.998 0.249 5.144 0.09000
  17 H042 H2 E -3.369 1.941 5.237 0.09000
  18 CC05 C2 M -3.358 0.867 7.140 -0.18000
  19 H051 H2 E -2.567 1.502 7.592 0.09000
  20 H052 H2 E -3.227 -0.177 7.497 0.09000
  21 CC06 C2 M -4.740 1.385 7.578 -0.18000
  22 H061 H2 E -5.540 0.758 7.128 0.09000
  23 H062 H2 E -4.876 2.435 7.241 0.09000
  24 CC07 C2 M -4.816 1.311 9.114 -0.18000
  25 H071 H2 E -3.995 1.918 9.553 0.09000
  26 H072 H2 E -4.695 0.256 9.439 0.09000
  27 CC08 C2 M -6.170 1.846 9.614 -0.18000
  28 H081 H2 E -6.997 1.247 9.177 0.09000
  29 H082 H2 E -6.294 2.907 9.306 0.09000
  30 CC09 C2 M -6.201 1.741 11.151 -0.18000
  31 H091 H2 E -5.362 2.328 11.580 0.09000
  32 H092 H2 E -6.086 0.678 11.452 0.09000
  33 CC10 C2 M -7.539 2.286 11.687 -0.18000
  34 H101 H2 E -8.380 1.705 11.253 0.09000
  35 H102 H2 E -7.651 3.352 11.397 0.09000
  36 CC11 C2 M -7.560 2.161 13.221 -0.18000
  37 H111 H2 E -6.713 2.736 13.653 0.09000
  38 H112 H2 E -7.452 1.093 13.509 0.09000
  39 CC12 C3 M -8.889 2.711 13.769 -0.27000
  40 H121 H3 E -9.742 2.138 13.347 0.09000
  41 H122 H3 E -9.003 3.779 13.483 0.09000
  42 H123 H3 E -8.910 2.616 14.876 0.09000

DONE
STOP
------------------------------------------------------------------------------------------------------------
CONTENT OF gold.in:

    1 0 2
AU1.dat
AU1 gold for the SAM
AU1.dat
AU1 XYZ 1
CHANGE IOMIT DU ALL
0.0
   1 DUMM DU M 0.000 0.000 0.000 0.00000
   2 DUMM DU M 1.449 0.000 0.000 0.00000
   3 DUMM DU M 1.522 111.100 0.000 0.00000
   4 AU1 A1 M -1.442 2.497 0.000 0.00000

DONE
STOP

-------------------------------------------------------------------------------------------------------------

CONTENT OF firstsamunitwithgold.pdb:

ATOM 1 AU C12 1 0.000 0.000 0.000 1.00 0.00 ML1
ATOM 2 S C12 1 0.018 -0.179 1.585 1.00 0.00 ML1
ATOM 3 CC01 C12 1 -0.216 -0.118 3.379 1.00 0.00 ML1
ATOM 4 H011 C12 1 0.535 0.570 3.823 1.00 0.00 ML1
ATOM 5 H012 C12 1 -0.074 -1.135 3.802 1.00 0.00 ML1
ATOM 6 CC02 C12 1 -1.636 0.386 3.704 1.00 0.00 ML1
ATOM 7 H021 C12 1 -2.389 -0.287 3.241 1.00 0.00 ML1
ATOM 8 H022 C12 1 -1.773 1.411 3.300 1.00 0.00 ML1
ATOM 9 CC03 C12 1 -1.820 0.399 5.233 1.00 0.00 ML1
ATOM 10 H031 C12 1 -1.058 1.067 5.689 1.00 0.00 ML1
ATOM 11 H032 C12 1 -1.680 -0.629 5.630 1.00 0.00 ML1
ATOM 12 CC04 C12 1 -3.227 0.902 5.606 1.00 0.00 ML1
ATOM 13 H041 C12 1 -3.998 0.249 5.144 1.00 0.00 ML1
ATOM 14 H042 C12 1 -3.369 1.941 5.237 1.00 0.00 ML1
ATOM 15 CC05 C12 1 -3.358 0.867 7.140 1.00 0.00 ML1
ATOM 16 H051 C12 1 -2.567 1.502 7.592 1.00 0.00 ML1
ATOM 17 H052 C12 1 -3.227 -0.177 7.497 1.00 0.00 ML1
ATOM 18 CC06 C12 1 -4.740 1.385 7.578 1.00 0.00 ML1
ATOM 19 H061 C12 1 -5.540 0.758 7.128 1.00 0.00 ML1
ATOM 20 H062 C12 1 -4.876 2.435 7.241 1.00 0.00 ML1
ATOM 21 CC07 C12 1 -4.816 1.311 9.114 1.00 0.00 ML1
ATOM 22 H071 C12 1 -3.995 1.918 9.553 1.00 0.00 ML1
ATOM 23 H072 C12 1 -4.695 0.256 9.439 1.00 0.00 ML1
ATOM 24 CC08 C12 1 -6.170 1.846 9.614 1.00 0.00 ML1
ATOM 25 H081 C12 1 -6.997 1.247 9.177 1.00 0.00 ML1
ATOM 26 H082 C12 1 -6.294 2.907 9.306 1.00 0.00 ML1
ATOM 27 CC09 C12 1 -6.201 1.741 11.151 1.00 0.00 ML1
ATOM 28 H091 C12 1 -5.362 2.328 11.580 1.00 0.00 ML1
ATOM 29 H092 C12 1 -6.086 0.678 11.452 1.00 0.00 ML1
ATOM 30 CC10 C12 1 -7.539 2.286 11.687 1.00 0.00 ML1
ATOM 31 H101 C12 1 -8.380 1.705 11.253 1.00 0.00 ML1
ATOM 32 H102 C12 1 -7.651 3.352 11.397 1.00 0.00 ML1
ATOM 33 CC11 C12 1 -7.560 2.161 13.221 1.00 0.00 ML1
ATOM 34 H111 C12 1 -6.713 2.736 13.653 1.00 0.00 ML1
ATOM 35 H112 C12 1 -7.452 1.093 13.509 1.00 0.00 ML1
ATOM 36 CC12 C12 1 -8.889 2.711 13.769 1.00 0.00 ML1
ATOM 37 H121 C12 1 -9.742 2.138 13.347 1.00 0.00 ML1
ATOM 38 H122 C12 1 -9.003 3.779 13.483 1.00 0.00 ML1
ATOM 39 H123 C12 1 -8.910 2.616 14.876 1.00 0.00 ML1
TER
ATOM 40 AU C12 2 -4.325 2.497 -0.012 1.00 0.00 ML2
ATOM 41 S C12 2 -4.368 2.438 1.754 1.00 0.00 ML2
ATOM 42 CC01 C12 2 -4.610 2.499 3.546 1.00 0.00 ML2
ATOM 43 H011 C12 2 -3.862 3.188 3.993 1.00 0.00 ML2
ATOM 44 H012 C12 2 -4.469 1.482 3.970 1.00 0.00 ML2
ATOM 45 CC02 C12 2 -6.032 3.001 3.864 1.00 0.00 ML2
ATOM 46 H021 C12 2 -6.781 2.328 3.396 1.00 0.00 ML2
ATOM 47 H022 C12 2 -6.168 4.026 3.459 1.00 0.00 ML2
ATOM 48 CC03 C12 2 -6.224 3.013 5.392 1.00 0.00 ML2
ATOM 49 H031 C12 2 -5.465 3.681 5.853 1.00 0.00 ML2
ATOM 50 H032 C12 2 -6.086 1.985 5.789 1.00 0.00 ML2
ATOM 51 CC04 C12 2 -7.634 3.515 5.758 1.00 0.00 ML2
ATOM 52 H041 C12 2 -8.402 2.862 5.291 1.00 0.00 ML2
ATOM 53 H042 C12 2 -7.774 4.554 5.388 1.00 0.00 ML2
ATOM 54 CC05 C12 2 -7.773 3.479 7.291 1.00 0.00 ML2
ATOM 55 H051 C12 2 -6.984 4.115 7.747 1.00 0.00 ML2
ATOM 56 H052 C12 2 -7.642 2.435 7.648 1.00 0.00 ML2
ATOM 57 CC06 C12 2 -9.158 3.996 7.722 1.00 0.00 ML2
ATOM 58 H061 C12 2 -9.955 3.368 7.268 1.00 0.00 ML2
ATOM 59 H062 C12 2 -9.292 5.046 7.385 1.00 0.00 ML2
ATOM 60 CC07 C12 2 -9.240 3.921 9.258 1.00 0.00 ML2
ATOM 61 H071 C12 2 -8.422 4.528 9.700 1.00 0.00 ML2
ATOM 62 H072 C12 2 -9.120 2.865 9.582 1.00 0.00 ML2
ATOM 63 CC08 C12 2 -10.597 4.456 9.752 1.00 0.00 ML2
ATOM 64 H081 C12 2 -11.422 3.856 9.311 1.00 0.00 ML2
ATOM 65 H082 C12 2 -10.719 5.516 9.444 1.00 0.00 ML2
ATOM 66 CC09 C12 2 -10.637 4.349 11.288 1.00 0.00 ML2
ATOM 67 H091 C12 2 -9.800 4.937 11.722 1.00 0.00 ML2
ATOM 68 H092 C12 2 -10.523 3.286 11.589 1.00 0.00 ML2
ATOM 69 CC10 C12 2 -11.977 4.893 11.817 1.00 0.00 ML2
ATOM 70 H101 C12 2 -12.816 4.312 11.378 1.00 0.00 ML2
ATOM 71 H102 C12 2 -12.089 5.960 11.526 1.00 0.00 ML2
ATOM 72 CC11 C12 2 -12.006 4.768 13.351 1.00 0.00 ML2
ATOM 73 H111 C12 2 -11.162 5.344 13.787 1.00 0.00 ML2
ATOM 74 H112 C12 2 -11.899 3.701 13.640 1.00 0.00 ML2
ATOM 75 CC12 C12 2 -13.339 5.317 13.892 1.00 0.00 ML2
ATOM 76 H121 C12 2 -14.189 4.743 13.466 1.00 0.00 ML2
ATOM 77 H122 C12 2 -13.452 6.385 13.606 1.00 0.00 ML2
ATOM 78 H123 C12 2 -13.366 5.222 14.999 1.00 0.00 ML2
TER
ATOM 79 AU C12 3 -4.325 7.492 0.000 1.00 0.00 ML3
ATOM 80 S C12 3 -4.418 7.575 1.702 1.00 0.00 ML3
ATOM 81 CC01 C12 3 -4.984 8.660 3.036 1.00 0.00 ML3
ATOM 82 H011 C12 3 -5.409 9.588 2.598 1.00 0.00 ML3
ATOM 83 H012 C12 3 -4.120 8.925 3.683 1.00 0.00 ML3
ATOM 84 CC02 C12 3 -6.058 7.941 3.873 1.00 0.00 ML3
ATOM 85 H021 C12 3 -5.642 7.000 4.293 1.00 0.00 ML3
ATOM 86 H022 C12 3 -6.931 7.693 3.233 1.00 0.00 ML3
ATOM 87 CC03 C12 3 -6.499 8.872 5.018 1.00 0.00 ML3
ATOM 88 H031 C12 3 -6.906 9.814 4.591 1.00 0.00 ML3
ATOM 89 H032 C12 3 -5.621 9.116 5.653 1.00 0.00 ML3
ATOM 90 CC04 C12 3 -7.581 8.195 5.882 1.00 0.00 ML3
ATOM 91 H041 C12 3 -7.190 7.245 6.304 1.00 0.00 ML3
ATOM 92 H042 C12 3 -8.476 7.971 5.262 1.00 0.00 ML3
ATOM 93 CC05 C12 3 -7.959 9.160 7.020 1.00 0.00 ML3
ATOM 94 H051 C12 3 -8.325 10.115 6.587 1.00 0.00 ML3
ATOM 95 H052 C12 3 -7.061 9.368 7.640 1.00 0.00 ML3
ATOM 96 CC06 C12 3 -9.059 8.548 7.907 1.00 0.00 ML3
ATOM 97 H061 C12 3 -8.704 7.590 8.343 1.00 0.00 ML3
ATOM 98 H062 C12 3 -9.969 8.352 7.301 1.00 0.00 ML3
ATOM 99 CC07 C12 3 -9.381 9.551 9.031 1.00 0.00 ML3
ATOM 100 H071 C12 3 -9.707 10.514 8.583 1.00 0.00 ML3
ATOM 101 H072 C12 3 -8.469 9.728 9.639 1.00 0.00 ML3
ATOM 102 CC08 C12 3 -10.501 9.004 9.935 1.00 0.00 ML3
ATOM 103 H081 C12 3 -10.185 8.039 10.385 1.00 0.00 ML3
ATOM 104 H082 C12 3 -11.422 8.837 9.337 1.00 0.00 ML3
ATOM 105 CC09 C12 3 -10.779 10.033 11.048 1.00 0.00 ML3
ATOM 106 H091 C12 3 -11.079 11.001 10.592 1.00 0.00 ML3
ATOM 107 H092 C12 3 -9.857 10.190 11.648 1.00 0.00 ML3
ATOM 108 CC10 C12 3 -11.907 9.525 11.963 1.00 0.00 ML3
ATOM 109 H101 C12 3 -11.613 8.553 12.415 1.00 0.00 ML3
ATOM 110 H102 C12 3 -12.834 9.377 11.368 1.00 0.00 ML3
ATOM 111 CC11 C12 3 -12.164 10.558 13.075 1.00 0.00 ML3
ATOM 112 H111 C12 3 -12.451 11.530 12.621 1.00 0.00 ML3
ATOM 113 H112 C12 3 -11.238 10.700 13.672 1.00 0.00 ML3
ATOM 114 CC12 C12 3 -13.298 10.063 13.993 1.00 0.00 ML3
ATOM 115 H121 C12 3 -13.018 9.094 14.457 1.00 0.00 ML3
ATOM 116 H122 C12 3 -14.227 9.918 13.401 1.00 0.00 ML3
ATOM 117 H123 C12 3 -13.481 10.804 14.801 1.00 0.00 ML3
TER
ATOM 118 AU C12 4 0.000 4.994 0.012 1.00 0.00 ML4
ATOM 119 S C12 4 -0.197 5.050 1.715 1.00 0.00 ML4
ATOM 120 CC01 C12 4 -0.760 6.135 3.050 1.00 0.00 ML4
ATOM 121 H011 C12 4 -1.188 7.062 2.612 1.00 0.00 ML4
ATOM 122 H012 C12 4 0.105 6.402 3.694 1.00 0.00 ML4
ATOM 123 CC02 C12 4 -1.831 5.415 3.891 1.00 0.00 ML4
ATOM 124 H021 C12 4 -1.412 4.475 4.309 1.00 0.00 ML4
ATOM 125 H022 C12 4 -2.706 5.165 3.253 1.00 0.00 ML4
ATOM 126 CC03 C12 4 -2.271 6.345 5.037 1.00 0.00 ML4
ATOM 127 H031 C12 4 -2.680 7.286 4.610 1.00 0.00 ML4
ATOM 128 H032 C12 4 -1.391 6.590 5.669 1.00 0.00 ML4
ATOM 129 CC04 C12 4 -3.348 5.668 5.904 1.00 0.00 ML4
ATOM 130 H041 C12 4 -2.955 4.719 6.325 1.00 0.00 ML4
ATOM 131 H042 C12 4 -4.245 5.443 5.287 1.00 0.00 ML4
ATOM 132 CC05 C12 4 -3.723 6.632 7.044 1.00 0.00 ML4
ATOM 133 H051 C12 4 -4.091 7.588 6.611 1.00 0.00 ML4
ATOM 134 H052 C12 4 -2.823 6.841 7.660 1.00 0.00 ML4
ATOM 135 CC06 C12 4 -4.820 6.020 7.933 1.00 0.00 ML4
ATOM 136 H061 C12 4 -4.464 5.062 8.369 1.00 0.00 ML4
ATOM 137 H062 C12 4 -5.732 5.823 7.330 1.00 0.00 ML4
ATOM 138 CC07 C12 4 -5.141 7.023 9.058 1.00 0.00 ML4
ATOM 139 H071 C12 4 -5.469 7.985 8.611 1.00 0.00 ML4
ATOM 140 H072 C12 4 -4.227 7.201 9.664 1.00 0.00 ML4
ATOM 141 CC08 C12 4 -6.257 6.475 9.967 1.00 0.00 ML4
ATOM 142 H081 C12 4 -5.938 5.510 10.415 1.00 0.00 ML4
ATOM 143 H082 C12 4 -7.180 6.307 9.371 1.00 0.00 ML4
ATOM 144 CC09 C12 4 -6.533 7.503 11.079 1.00 0.00 ML4
ATOM 145 H091 C12 4 -6.834 8.471 10.624 1.00 0.00 ML4
ATOM 146 H092 C12 4 -5.609 7.660 11.677 1.00 0.00 ML4
ATOM 147 CC10 C12 4 -7.659 6.995 11.998 1.00 0.00 ML4
ATOM 148 H101 C12 4 -7.363 6.023 12.449 1.00 0.00 ML4
ATOM 149 H102 C12 4 -8.587 6.847 11.406 1.00 0.00 ML4
ATOM 150 CC11 C12 4 -7.913 8.028 13.112 1.00 0.00 ML4
ATOM 151 H111 C12 4 -8.201 9.000 12.659 1.00 0.00 ML4
ATOM 152 H112 C12 4 -6.985 8.170 13.706 1.00 0.00 ML4
ATOM 153 CC12 C12 4 -9.043 7.532 14.032 1.00 0.00 ML4
ATOM 154 H121 C12 4 -8.761 6.562 14.494 1.00 0.00 ML4
ATOM 155 H122 C12 4 -9.974 7.386 13.442 1.00 0.00 ML4
ATOM 156 H123 C12 4 -9.225 8.271 14.841 1.00 0.00 ML4
TER
ATOM 157 AU1 AU1 5 -1.442 2.497 0.000 1.00 0.00 A1
TER
ATOM 158 AU1 AU1 6 -8.651 0.000 -0.035 1.00 0.00 A2
TER
ATOM 159 AU1 AU1 7 -7.209 2.497 -0.023 1.00 0.00 A3
TER
ATOM 160 AU1 AU1 8 -5.767 0.000 -0.023 1.00 0.00 A4
TER
ATOM 161 AU1 AU1 9 -2.884 4.995 0.000 1.00 0.00 A5
TER
ATOM 162 AU1 AU1 10 -5.767 4.995 -0.012 1.00 0.00 A6
TER
ATOM 163 AU1 AU1 11 -8.651 4.995 -0.023 1.00 0.00 A7
TER
ATOM 164 AU1 AU1 12 -1.442 7.492 0.012 1.00 0.00 A8
TER
ATOM 165 AU1 AU1 13 -2.884 0.000 -0.012 1.00 0.00 A9
TER
ATOM 166 AU1 AU1 14 -7.209 7.492 -0.012 1.00 0.00 A10
TER
ATOM 167 AU1 AU1 15 0.009 1.670 -2.351 1.00 0.00 A11
TER
ATOM 168 AU1 AU1 16 -2.874 1.670 -2.362 1.00 0.00 A12
TER
ATOM 169 AU1 AU1 17 -5.758 1.670 -2.374 1.00 0.00 A13
TER
ATOM 170 AU1 AU1 18 -8.641 1.670 -2.385 1.00 0.00 A14
TER
ATOM 171 AU1 AU1 19 -1.432 4.168 -2.351 1.00 0.00 A15
TER
ATOM 172 AU1 AU1 20 -4.316 4.168 -2.362 1.00 0.00 A16
TER
ATOM 173 AU1 AU1 21 -7.200 4.168 -2.374 1.00 0.00 A17
TER
ATOM 174 AU1 AU1 22 0.009 6.665 -2.339 1.00 0.00 A18
TER
ATOM 175 AU1 AU1 23 -2.874 6.665 -2.351 1.00 0.00 A19
TER
ATOM 176 AU1 AU1 24 -5.758 6.665 -2.362 1.00 0.00 A20
TER
ATOM 177 AU1 AU1 25 -8.641 6.665 -2.374 1.00 0.00 A21
TER
ATOM 178 AU1 AU1 26 -1.432 9.162 -2.339 1.00 0.00 A22
TER
ATOM 179 AU1 AU1 27 -4.316 9.162 -2.351 1.00 0.00 A23
TER
ATOM 180 AU1 AU1 28 -7.200 9.162 -2.362 1.00 0.00 A24
TER
ATOM 181 AU1 AU1 29 -1.423 0.843 -4.713 1.00 0.00 A25
TER
ATOM 182 AU1 AU1 30 -4.307 0.843 -4.724 1.00 0.00 A26
TER
ATOM 183 AU1 AU1 31 -7.190 0.843 -4.736 1.00 0.00 A27
TER
ATOM 184 AU1 AU1 32 0.019 3.341 -4.701 1.00 0.00 A28
TER
ATOM 185 AU1 AU1 33 -2.865 3.341 -4.713 1.00 0.00 A29
TER
ATOM 186 AU1 AU1 34 -5.748 3.341 -4.724 1.00 0.00 A30
TER
ATOM 187 AU1 AU1 35 -8.632 3.341 -4.736 1.00 0.00 A31
TER
ATOM 188 AU1 AU1 36 -1.423 5.838 -4.701 1.00 0.00 A32
TER
ATOM 189 AU1 AU1 37 -4.307 5.838 -4.713 1.00 0.00 A33
TER
ATOM 190 AU1 AU1 38 -7.190 5.838 -4.724 1.00 0.00 A34
TER
ATOM 191 AU1 AU1 39 0.019 8.335 -4.690 1.00 0.00 A35
TER
ATOM 192 AU1 AU1 40 -2.865 8.335 -4.701 1.00 0.00 A36
TER
ATOM 193 AU1 AU1 41 -5.748 8.335 -4.713 1.00 0.00 A37
TER
ATOM 194 AU1 AU1 42 -8.633 8.335 -4.725 1.00 0.00 A38
TER
END

-----------------------------------------------------------------------------------------------------------------

SECTION OF GTG.top SHOWING THE NAN ERROR:

%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
  4.94082677E+02 NAN 1.41608507E+07
4.38119292E+04 NAN
  1.06871988E+06 1.21779344E+03 NAN 6.75488201E+04
2.52156288E+03
             NAN 3.36763666E+05 NAN NAN
4.39306376E+03
             NAN 4.43074699E+06 NAN NAN
1.00070887E+05
  1.38006405E+06 1.24516301E+03 NAN 6.90669607E+04
2.57823429E+03
             NAN NAN 2.63617938E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
  1.24158687E+01 NAN 5.15968984E+03
1.09493326E+02 NAN
  5.06451153E+02 1.42051601E+01 NAN 9.90791706E+01
1.48962255E+01
             NAN 4.06447605E+02 NAN NAN
2.37131221E+01
             NAN 1.81185588E+03 NAN NAN
1.39091977E+02
  6.34806034E+02 1.45244170E+01 NAN 1.01305947E+02
1.52310139E+01
             NAN NAN 1.55733266E+01

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu