Fwd: Fwd: hi

From: kanchi subbarao rao (ksubbu85_at_gmail.com)
Date: Wed Jun 01 2011 - 13:32:41 CDT

---------- Forwarded message ----------
From: kanchi subbarao rao <ksubbu85_at_gmail.com>
Date: Wed, Jun 1, 2011 at 9:51 PM
Subject: Fwd: Fwd: hi
To: fzhu_at_wag.caltech.edu

---------- Forwarded message ----------
From: kanchi subbarao rao <ksubbu85_at_gmail.com>
Date: Wed, Jun 1, 2011 at 10:36 AM
Subject: Re: Fwd: hi
To: Fangqiang Zhu <fzhu_at_wag.caltech.edu>

thank you Fangqiang Zhu
it is now working. but i have a doubt "in vmd also we always call the psfgen
while creating a psf and pdb files.it is working then with out namd. what
is the difference between that and this ?

*what changes i have to do in make_arm.tcl to create graphene-sheet instead
of nano tubue?*
shall you sagest me ?

thanks
subbarao kanchi.

On Tue, May 31, 2011 at 7:11 PM, Fangqiang Zhu <fzhu_at_wag.caltech.edu> wrote:

> To use this script you need to install psfgen first, which usually
> comes with the NAMD binary...
>
> On Tue, 31 May 2011, kanchi subbarao rao wrote:
>
> > ---------- 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 ,
> >
> > 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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