Output File Output File
DISCOVER Molecular Simulation Program
Version: 95.0 Beta
Date: Tue Jan 24 18:06:51 1995
User Name: kit
Host Name: iris24
Host Type: iris
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Licensed by BIOSYM Technologies to
BIOSYM SAN DIEGO
----------------------------------------------------------------
NLS: License for Discover_Pgm Checked Out
randomSeed is set to 999613
Line 12:BTCL> proc fixorientation {molecule1 ca1 molecule2 ca2 mindist \
axis1var point1var axis2var point2var} {
upvar 1 $axis1var axis1
upvar 1 $point1var point1
upvar 1 $axis2var axis2
upvar 1 $point2var point2
# find axes for molecules 1 and 2 by finding the least square fit lines
# through the backbone atoms
molGeom get lsqLine axis1 $ca1
molGeom get lsqLine axis2 $ca2
# find the angle between two lines
geometry ang12 angle $axis1 $axis2
# find the cross product between two lines
# so the axis of rotation can be defined
geometry vec1 vector $axis1
geometry vec2 vector $axis2
vector vec3 cross $vec1 $vec2
# rotate molecule2 along the axis with origin at centroid of axis2
# and direction of vector perpendicular to plane defined by axis1 and axis2
# to make the two helices parallel
geometry point1 point $axis1
geometry point2 point $axis2
geometry rotateaxis "line $point2 $vec3"
vector ang12 negate $ang12
# Molgeom command takes angles in degrees while geometry command takes angles
# in radian
vector ang12 degree $ang12
molGeom rotate $rotateaxis $ang12 $molecule2
# find the new axis of molecule 2
molGeom get lsqLine axis2 $ca2
geometry vec2 vector $axis2
geometry point2 point $axis2
# find the vector which passes centroid of axis1 and perpendicular to 2
geometry vect vector $axis2 $point1
geometry perline "line $point1 $vect"
geometry dist distance $point2 $perline
vector dist negate $dist
# translate the molecule along its own axis so
# two centroids of the axes will be the shortest distance apart
molGeom translate $vec2 $dist $molecule2
#
# find the distance between the two helices and put them at $mindist apart
#
geometry point2 point $axis2
geometry direction vector $axis1 $point2
geometry dist distance $point1 $axis2
vector dist subtract $mindist $dist
molGeom translate $direction $dist $molecule2
# find the new axis of molecule 2
molGeom get lsqLine axis2 $ca2
geometry point2 point $axis2
}
Line 87:BTCL> proc writeheading { tblfile } {
puts $tblfile "!BIOSYM output_table 1"
puts $tblfile "#"
puts $tblfile "TITLE: Frame Number"
puts $tblfile "MEASUREMENT TYPE: Number"
puts $tblfile "UNITS OF MEASUREMENT: none"
puts $tblfile "FUNCTION: Frame_number"
puts $tblfile "#"
puts $tblfile "TITLE: Rotate angle"
puts $tblfile "MEASUREMENT TYPE: Angle"
puts $tblfile "UNITS OF MEASUREMENT: radian"
puts $tblfile "FUNCTION: Rotate_angle"
puts $tblfile "#"
puts $tblfile "TITLE: Spin angle"
puts $tblfile "MEASUREMENT TYPE: Angle"
puts $tblfile "UNITS OF MEASUREMENT: radian"
puts $tblfile "FUNCTION: Spin_angle"
puts $tblfile "#"
puts $tblfile "TITLE: Separation distance"
puts $tblfile "MEASUREMENT TYPE: Separation"
puts $tblfile "UNITS OF MEASUREMENT: Angstroms"
puts $tblfile "FUNCTION: Separation"
puts $tblfile "#"
puts $tblfile "TITLE: Total energy"
puts $tblfile "MEASUREMENT TYPE: Energy"
puts $tblfile "UNITS OF MEASUREMENT: kcal/mol"
puts $tblfile "FUNCTION: Total energy"
puts $tblfile "#"
puts $tblfile "#"
}
Line 121:BTCL> begin
INPUT FILES
___________
File Type Name
--------- ----
Forcefield /ax10/bioroot/develop/release950/irix51r4/biosym_lib/cvff.frc
Molecular data helix.mdf
Coordinate helix.car
Line 125:BTCL> $mindist = 10.0
Line 126:BTCL> $maxdist = 15.0
Line 127:BTCL> $nummove = 5
Line 128:BTCL> $moveinc = ( $maxdist - $mindist ) / $nummove
Line 132:BTCL> $startspin = 0
Line 133:BTCL> $endspin = 360.0
Line 134:BTCL> $numspin = 4
Line 135:BTCL> $spininc = ( $endspin - $startspin ) / $numspin
Line 140:BTCL> $startrotate = 0
Line 141:BTCL> $endrotate = 360
Line 142:BTCL> $numrotate = 4
Line 143:BTCL> $rotateinc = ( $endrotate - $startrotate ) / $numrotate
Line 147:BTCL> $nframe = 0
Line 148:BTCL> $distance = $mindist
Line 152:BTCL> set tblfile [ open $PROJECT.tbl w ]
Line 153:BTCL> writeheading $tblfile
Line 157:BTCL> set molecule1 "HELIX_1:*:Atom;*"
Line 158:BTCL> set molecule2 "HELIX_2:*:Atom;*"
Line 162:BTCL> subset define Subset "HELIX_1:*:backbone1" "CA,N,C"
Line 163:BTCL> subset define Subset "HELIX_2:*:backbone2" "CA,N,C"
Line 164:BTCL> subset get helix1ca "HELIX_1:*:backbone1"
Line 165:BTCL> subset get helix2ca "HELIX_2:*:backbone2"
Line 172:BTCL> fixorientation $molecule1 $helix1ca $molecule2 $helix2ca $mindist \
axis1 point1 axis2 point2
Line 177:BTCL> echo $axis1
geometry#5
Line 178:BTCL> echo axis1 = [geometry axis1]
axis1 = line {{11.0926 17.2649 3.27548}} {{-0.821539 0.123481 0.55662}}
Line 179:BTCL> echo axis2 = [geometry axis2]
axis2 = line {{5.90624 11.5912 -3.12062}} {{-0.821539 0.123481 0.55662}}
Line 180:BTCL> geometry dist distance $axis1 $axis2
Line 181:BTCL> echo line distance = [geometry dist]
line distance = point 10.0
Line 182:BTCL> geometry dist distance $point1 $point2
Line 183:BTCL> echo point distance = [geometry dist]
point distance = point 10.0
Line 188:BTCL> writeFile coordinate filename = .cor
Line 198:BTCL> for {$i = 0} {$i < $numrotate} {incr i} {
$rotateang = $startrotate + $i * $rotateinc
if {$i > 0} {
molGeom rotate $axis1 $rotateinc $molecule2
}
# find axis of molecule2 and the direction of translation again
molGeom get lsqLine axis2 $helix2ca
geometry point2 point $axis2
geometry transdirect vector $axis1 $point2
#
# rotate molecule 2 around its own axis
#
for {$j = 0} {$j <= $numspin} {incr j} {
$spinang = $startspin + $j * $spininc
if {$j > 0} {
molGeom rotate $axis2 $spininc $molecule2
}
# move molecule2 so it is at minimum distance from molecule 1 again
$movedist = $mindist - $distance
molGeom translate $transdirect $movedist $molecule2
#
#
# move molecule 2 along the direction defined by the perpendicular direction
# between axis 1 and axis 2
#
for {$k = 0} {$k <= $nummove} {incr k} {
if {$k > 0} {
molGeom translate $transdirect $moveinc $molecule2
}
# find the new axis of molecule2 again
molGeom get lsqLine axis2 $helix2ca
# find the distances between two axes
geometry dist distance $axis1 $axis2
set distance [object dist]
if {$j == $numspin} continue
# evaluate energy
set energyval [energy]
# write the coordinates in an archive file
$nframe = $nframe + 1
writeFile archive frame = $nframe filename = .arc
# write the heading in output file
if {$nframe == 1} {
puts [ format " \n " ]
puts [ format " %12s %12s %12s %12s %12s " \
Frame Rotate Spin Distance Energy ]
puts [ format " \n " ]
}
# write the energy into the output file
puts [ format " %12d %12.2f %12.2f %12.2f %12.6g " \
$nframe $rotateang $spinang $distance $energyval ]
# write the energy into the table file for sorting and graphing
puts $tblfile "$nframe $rotateang $spinang \
$distance $energyval"
}
}
}
MOLECULAR TOPOLOGY
__________________
Number of molecules: 2
Number of residues: 18
Number of atoms: 286
Number of atom types: 16
Number of bonds: 288
Number of angles: 510
Number of torsions: 744
Number of out-of-planes: 60
FORCEFIELD OPTIONS
__________________
Name : cvff_nocross_nomorse
# of automatic parameters : 2
NONBOND ENERGY CUTOFFS
______________________
Cutoff (A) Spline Width (A) Buffer Width (A)
vdW 9.50 1.00 0.50
Coulomb 9.50 1.00 0.50
Summation method for vdW : Group based
Summation method for Coulomb : Group based
Dielectric : 1.00
Frame Rotate Spin Distance Energy
1 0.00 0.00 10.00 555.251
2 0.00 0.00 11.00 463.568
3 0.00 0.00 12.00 463.233
4 0.00 0.00 13.00 465.107
5 0.00 0.00 14.00 466.004
6 0.00 0.00 15.00 466.262
7 0.00 90.00 10.00 483.799
8 0.00 90.00 11.00 461.901
9 0.00 90.00 12.00 464.173
10 0.00 90.00 13.00 465.445
11 0.00 90.00 14.00 466.028
12 0.00 90.00 15.00 466.279
13 0.00 180.00 10.00 513.406
14 0.00 180.00 11.00 464.056
15 0.00 180.00 12.00 461.837
16 0.00 180.00 13.00 464.364
17 0.00 180.00 14.00 465.585
18 0.00 180.00 15.00 466.18
19 0.00 270.00 10.00 7.32865e+13
20 0.00 270.00 11.00 3.17888e+06
21 0.00 270.00 12.00 702.131
22 0.00 270.00 13.00 460.31
23 0.00 270.00 14.00 463.605
24 0.00 270.00 15.00 465.42
25 90.00 0.00 10.00 8.54363e+14
26 90.00 0.00 11.00 9.94178e+08
27 90.00 0.00 12.00 5.87639e+09
28 90.00 0.00 13.00 21744.3
29 90.00 0.00 14.00 504.679
30 90.00 0.00 15.00 465.402
31 90.00 90.00 10.00 902.451
32 90.00 90.00 11.00 468.082
33 90.00 90.00 12.00 464.086
34 90.00 90.00 13.00 465.32
35 90.00 90.00 14.00 465.973
36 90.00 90.00 15.00 466.242
37 90.00 180.00 10.00 462.237
38 90.00 180.00 11.00 461.969
39 90.00 180.00 12.00 464.479
40 90.00 180.00 13.00 465.598
41 90.00 180.00 14.00 466.121
42 90.00 180.00 15.00 466.308
43 90.00 270.00 10.00 468.932
44 90.00 270.00 11.00 461.411
45 90.00 270.00 12.00 464.368
46 90.00 270.00 13.00 465.656
47 90.00 270.00 14.00 466.116
48 90.00 270.00 15.00 466.365
49 180.00 0.00 10.00 461.994
50 180.00 0.00 11.00 464.431
51 180.00 0.00 12.00 465.468
52 180.00 0.00 13.00 465.82
53 180.00 0.00 14.00 465.974
54 180.00 0.00 15.00 466.215
55 180.00 90.00 10.00 4.67907e+09
56 180.00 90.00 11.00 3.24332e+09
57 180.00 90.00 12.00 5.67121e+12
58 180.00 90.00 13.00 6.39336e+06
59 180.00 90.00 14.00 1494.38
60 180.00 90.00 15.00 469.662
61 180.00 180.00 10.00 1831.38
62 180.00 180.00 11.00 477.844
63 180.00 180.00 12.00 463.923
64 180.00 180.00 13.00 465.019
65 180.00 180.00 14.00 465.937
66 180.00 180.00 15.00 466.263
67 180.00 270.00 10.00 1.34607e+06
68 180.00 270.00 11.00 1217.02
69 180.00 270.00 12.00 465.681
70 180.00 270.00 13.00 464.989
71 180.00 270.00 14.00 465.877
72 180.00 270.00 15.00 466.216
73 270.00 0.00 10.00 733182
74 270.00 0.00 11.00 936.203
75 270.00 0.00 12.00 465.181
76 270.00 0.00 13.00 465.228
77 270.00 0.00 14.00 465.961
78 270.00 0.00 15.00 466.282
79 270.00 90.00 10.00 462.073
80 270.00 90.00 11.00 461.752
81 270.00 90.00 12.00 464.508
82 270.00 90.00 13.00 465.682
83 270.00 90.00 14.00 466.107
84 270.00 90.00 15.00 466.378
85 270.00 180.00 10.00 3.76667e+11
86 270.00 180.00 11.00 15872.2
87 270.00 180.00 12.00 484.785
88 270.00 180.00 13.00 460.656
89 270.00 180.00 14.00 464.134
90 270.00 180.00 15.00 465.595
91 270.00 270.00 10.00 151182
92 270.00 270.00 11.00 5985.69
93 270.00 270.00 12.00 1062.83
94 270.00 270.00 13.00 502.071
95 270.00 270.00 14.00 465.245
96 270.00 270.00 15.00 466.17
Total time used by DISCOVER: 49.46 secs
Completion date: Tue Jan 24 18:07:52 1995
Exiting Discover: status OK.
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