Greetings,
I'm trying to explore rotational steric hindrance with partial success. From
the console, this series of commands:
minimize constraint {C5} {C3} {C1} {H6} 60 // or whatever angle is
indicated
minimize
minimize energy
work as advertised. I can:
rotate branch {C3} {C1} 60 60
and repeat the minimization at a new torsion angle. Of course, I want to use
the power of Jmol script to automate the investigation. When I run these lines:
zap; load SYNC "file:///C:/Compchem/s-pentane/spentane.xyz"
rotdeg = 120
var steps=360/rotdeg
measure delete
measure {C5}{C3}{C1}{H6}
for (var i=0;i<steps;i++) {
rotate branch {C3} {C1} @rotdeg 60
conang = getproperty("measurementinfo[1].value")
print conang
script inline ("minimize constraint {C5} {C3} {C1} {H6} @conang")
minimize Steps 500
minimize
show minimization
minimize energy }
either as:
script "C:\Compchem\s-pentane\rotation.spt"
or by pasting into the console, I get rotations, but no minimization. It
prints the angle, reports the Initial MMFF and the "show minimization" report
has a section for contraints, although none are specified:
C O N S T R A I N T S
---------------------
---------------------
Not a wiggle do I get from the molecule as it breezes around the circle. Any
ideas out there?
Thanks,
George Whitwell
NCWC - Chemistry
For the sake of completeness, "spentane.xyz" is pasted here:
17
C 0.00679 0.03015 0.00260
C 0.92788 0.92359 0.83193
C -0.84948 -0.88283 0.88567
C -0.88496 0.87921 -0.90110
C -0.04442 -1.81120 1.79096
H 0.63109 -0.60981 -0.63251
H 1.47915 1.61518 0.19195
H 1.65692 0.34451 1.39972
H 0.34164 1.51743 1.53978
H -1.54380 0.25498 -1.50830
H -0.29104 1.50114 -1.57356
H -1.51253 1.54194 -0.29849
H -1.49875 -1.48148 0.23976
H -1.51200 -0.25707 1.49472
H 0.49906 -1.25500 2.55575
H 0.68519 -2.38126 1.21053
H -0.69411 -2.52260 2.30225
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