This is a script
to produce vibrational pdb file to be animated by Xmol. It requires the
ef.dump file it is initiated by typing
tclsh X_ef.ani > X_ef.log & at the prompt
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set
env(GRACE_LIB) /users/organic/guiseppe/temp source
$env(GRACE_LIB)/grace.tcl init i n |
START GRACE
PROCESS tell the script
were grace is situated and get it going |
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source ef.dump |
Now source the ef
file from a ts searching script |
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set symbols
"C H H H O C H H O H H Cl" |
Now we must tell
grace what the atomic symbols are as they are not stored in the ef.dump file |
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list>array
list=symbols array=atsy |
Set symbols into
an array atsy |
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la symm matrix=h la eign matrix=h |
Diagonalise the
Hessian, putting the vectors into roots and values into values |
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pmatrix
matrix=values |
print out the
values |
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Define a
procedure for writing out pdb file |
proc pdb_write
{pos atsy outf}{ |
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call by reference |
upvar $pos posv
$atsy atsyv |
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p>xyz p=posv
x=xv y=yv z=zv |
convert position
vector into xyz |
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set c 0 foreach i [array
names xv] { incr c puts $outf
[format {%-4s %5i %2s%2s %-4s%5i %8.3f%8.3f%8.3f%6.2f%6.2f} ATOM $c
$atsyv($c) "" REAC 1 $xv($c) $yv($c) $zv($c) 0.0 0.0] } puts $outf END } |
send out section
to pdb file |
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set c 0 foreach i [array
names roots] { incr c |
loop through all
eign values and vectors and make an animation of each |
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if {$c == 2}
break |
c = the number of
pdb files required minus one |
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list>array
list=roots($c) array=move |
make the root
into a veticle vector |
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la mplm
matrixl=move matrixr=x result=plus |
add it to the
position vector |
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la mbys
matrix=move scale=-1.0 result=mmove la mplm
matrixl=mmove matrixr=x result=minus |
subtract it to
the position vector |
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set file [open
X_ts_vib[set c].pdb w] |
Open the pdb file
and name it |
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pdb_write minus
atsy $file |
write out minus |
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pdb_write x atsy
$file |
write out start |
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pdb_write plus
atsy $file |
write out plus |
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pdb_write x atsy
$file |
write out start |
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close $file } |
close file |
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# EOF |
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