RE: psf creating for carbon nanotube

From: JC Gumbart (
Date: Sun Aug 15 2010 - 07:52:34 CDT

You can also check out the latest version of the Nanotubes tutorial here:



From: [] On Behalf
Of Jian Liu
Sent: Sunday, August 15, 2010 7:41 AM
To: namd-l; sara
Subject: Re: namd-l: psf creating for carbon nanotube


Dear Sara
I've write a script for SWNT'psf generating, it would be helpful for you.

# Tcl Script for Preparing pdb/psf of SWNT
# Programed by bay <bay__gulf618 at sina dot com> on June 22, 2010
# Usage: nanotube2 <l> <n> <m> [<output>] after source this script

package require nanotube
package require psfgen
proc writetop {{op ""}} {
  if {$op=="del"} {
    file delete
  } else {
    set fz [open "" w]
    puts $fz "* >>> Top File for C Cluster<<< "
    puts $fz "0 1 "
    puts $fz "MASS 21 CA 12.01100 C \n "
    puts $fz "RESI CNT 0.00 "
    puts $fz "GROUP "
    puts $fz "ATOM C CA 0.00 \n "
    puts $fz "PRES LINC 0.00 "
    puts $fz "BOND 1C 2C \n "
    puts $fz "END "
    close $fz

proc nanotube2 {length n m {output nanotube}} {
  nanotube -l $length -n $n -m $m
  set sel1 [atomselect top all]
  $sel1 set resid [$sel1 get index]
  $sel1 writepdb tmp1.pdb

  segment CCC {pdb tmp1.pdb}
  set xyz [$sel1 get {x y z}]
  foreach c1 [$sel1 get resid] {
    foreach c2 [$sel1 get resid] {
      set dist [vecdist [lindex $xyz $c1] [lindex $xyz $c2]]
      if {$c1 < $c2 && $dist < 1.8} {
        patch LINC CCC:$c1 CCC:$c2
  coordpdb tmp1.pdb CCC
  regenerate angles dihedrals
  writepdb ${output}.pdb
  writepsf ${output}.psf
  writetop del

Jian Liu
Master-degree Graduate Candidate Majoring in Molecular Modelling
Outstanding Students and PhD. Wanted, CV:

----- Original Message -----
From: sara <>
Subject: namd-l: psf creating for carbon nanotube
Date: 2010-8-15 15:48:36

Hi All

I want to simulate carbon nanotube but I have a problem.

I make it's pdb file but when I want to make the psf file it gives error. it
says the topology file is not match to CNT.

please guid me , which topology file I shoud load for this case.

if somebody has this file or the like file, please send for me.



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