From: kanchi subbarao rao (ksubbu85_at_gmail.com)
Date: Tue May 31 2011 - 05:10:32 CDT
---------- Forwarded message ----------
From: kanchi subbarao rao <ksubbu85_at_gmail.com>
Date: Tue, May 31, 2011 at 11:24 AM
Subject: Fwd: hi
To: jordi_at_ks.uiuc.edu
---------- Forwarded message ----------
From: kanchi subbarao rao <ksubbu85_at_gmail.com>
Date: Tue, May 31, 2011 at 11:23 AM
Subject: hi
To: jordi_at_ks.uiuc.edu
hi jordi,
i am doing nanotubes tutorial, in that to build the nano tubes
there is given a make_arm.tcl file.
that is given below
# Written by Fangqiang Zhu, 6/3/2002
# Make a m*m nanotube with length n.
# Write to $output.psf and $output.pdb
proc make_arm {m n output} {
# Bond length
set a 1.3750
set PI 3.141592654
set tt [expr 2*$PI/(3*$m)]
set r [expr $a/(2*sin($PI/3/$m))]
set fd_top [open temp_armchair.top w]
# Version number
puts $fd_top "0 0"
puts $fd_top "MASS 1 CA 12.01100 C"
puts $fd_top "AUTO ANGLES DIHE"
puts $fd_top "RESI ARM 0.00"
set fd_pgn [open temp_armchair.pgn w]
puts $fd_pgn "topology temp_armchair.top"
puts $fd_pgn "segment NT {residue 1 ARM}"
# Define the atom names for each carbon
set ind 0
for {set i 0} {$i<$n} {incr i} {
for {set j 0} {$j<$m} {incr j} {
for {set k 0} {$k<2} {incr k} {
if {$ind > 99} {
set name($i,$j,$k) C$ind
} elseif {$ind > 9} {
set name($i,$j,$k) C0$ind
} else {
set name($i,$j,$k) C00$ind
}
incr ind
}
}
}
for {set i 0} {$i<$n} {incr i} {
set z [expr ($i-($n-1)/2.0)*sqrt(3)/2*$a]
set t0 [expr ($i%2==0)?0:1.5*$tt]
for {set j 0} {$j<$m} {incr j} {
puts $fd_top "ATOM $name($i,$j,0) CA 0.00"
set t [expr $t0+(3*$j-0.5)*$tt]
puts $fd_pgn "coord NT 1 $name($i,$j,0) {[expr $r*cos($t)] [expr
$r*sin($t)] $z}"
puts $fd_top "ATOM $name($i,$j,1) CA 0.00"
set t [expr $t0+(3*$j+0.5)*$tt]
puts $fd_pgn "coord NT 1 $name($i,$j,1) {[expr $r*cos($t)] [expr
$r*sin($t)] $z}"
puts $fd_top "BOND $name($i,$j,0) $name($i,$j,1)"
if {$i%2 == 1} {
set ii [expr $i-1]
set jj [expr ($j+1)%$m]
puts $fd_top "BOND $name($ii,$j,1) $name($i,$j,0)"
puts $fd_top "BOND $name($ii,$jj,0) $name($i,$j,1)"
} elseif {$i > 0} {
set ii [expr $i-1]
set jj [expr ($j-1)%$m]
puts $fd_top "BOND $name($ii,$jj,1) $name($i,$j,0)"
puts $fd_top "BOND $name($ii,$j,0) $name($i,$j,1)"
}
}
}
puts $fd_pgn "writepsf $output.psf"
puts $fd_pgn "writepdb $output.pdb"
close $fd_top
close $fd_pgn
exec psfgen temp_armchair.pgn
exec rm temp_armchair.top
exec rm temp_armchair.pgn
}
while building nano tube in tcl-console by the commands
*make arm 6 12 nanotube*
*
*
i am getting the error *couldn't execute "psfgen": no such file or
directory *
i can not debug this error shall you helpme?
thanking you
subbarao kanchi.
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