VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Dec 06 2015 - 07:26:56 CST

On Sun, Dec 6, 2015 at 8:02 AM, zeynab hoseyni <zmhoseyni_at_gmail.com> wrote:
> Dear all,
>
> I try to produce psf and pdb files for carbon nanotubes using the script
> (make_arm.tcl) provided
> in the "Simulation of Water Permeation Through Nanotubes" tutorial. I source
> the script and then
> run the command make_arm 6 12 nanotube within tk console but receiveing the
> following error:
> couldn't execute "psfgen": no such file or directory
>
> The psfgen is installed within vmd since when I try the command:
> package require psfgen
> 1.6
> as you see, the version of the psfgen is given.. My vmd version is 1.9.
> Can you help me what is wrong?

the script below expects to use the standalone psfgen executable in
your path and call it as an external command. it does not use the
plugin version of psfgen.
the date on the script hints that it was written long before psfgen
was interfaced to be a vmd plugin.

axel.

>
> I copy the make_arm.tcl script here:
>
> # 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
> }
>
> Thanks in advance for your help,
> Zeynab 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.