VMD-L Mailing List

From: zeynab hoseyni (zmhoseyni_at_gmail.com)
Date: Sun Dec 06 2015 - 07:46:33 CST

Hi Axel,

I put the psfgen binary in /usr/local/bin/ and now it is working well.
Thanks for your help.

All the Best,
Zeynab

On Sun, Dec 6, 2015 at 1:26 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>