PSFGEN problems in nanotube tutorial

From: David L. Azevedo (david888_at_uol.com.br)
Date: Fri Oct 01 2004 - 01:36:36 CDT

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I am trying to work with nanotubes using NAMD and VMD. I have got the
'Simulation of water permeation through nanotubes' tutorial files from
(http://www.ks.uiuc.edu/Training/Tutorials/science/nanotubes/nanotubes-html/index.html)
and I´ve tried
to generate the nanotubes.psf file from the nanotubes.pdb file, I was
using the following
commands:

package require psfgen
topology par_nanotubes.inp
coordpdb nanotubes.pdb
writepdb nano.pdb
writepsf nano.psf

And I obtain many errors like this:

PSFGEN from NAMD 2.5 for Win32-i686
reading topology file par_nanotubes.inp

 This is a reduced version of the CHARMM22 parameter file for
 a nanotube simulation in water

ERROR! Unusual CHARMM version record.
ERROR! FAILED TO RECOGNIZE CA
ERROR! FAILED TO RECOGNIZE HT
ERROR! FAILED TO RECOGNIZE OT
ERROR! Failed to parse angle statement.
ERROR! FAILED TO RECOGNIZE CA
ERROR! FAILED TO RECOGNIZE HT
ERROR! Failed to parse dihedral statement.
ERROR! FAILED TO RECOGNIZE CA
ERROR! FAILED TO RECOGNIZE NONBONDED
ERROR! FAILED TO RECOGNIZE CUTNB
ERROR! FAILED TO RECOGNIZE CA
ERROR! FAILED TO RECOGNIZE HT
ERROR! FAILED TO RECOGNIZE OT
ERROR! FAILED TO RECOGNIZE HBOND
reading coordinates from pdb file nanotubes.pdb
no segment NT1
Warning: failed to set coordinate for atom C000 ARM:1 NT1
no segment NT1
Warning: failed to set coordinate for atom C001 ARM:1 NT1
no segment NT1

until the end of the nanotubes.pdb file:

Info: writing pdb file nano.pd
Info: pdb file complete.
Info: writing psf file nano.ps
total of 0 atoms
total of 0 bonds
total of 0 angles
total of 0 dihedrals
total of 0 impropers
Info: psf file complete.

I would like to know how to solve this problem, because I want to
generate my own
nanotubes 'pdb file' and try to do other kinds of simulations in NAMD
and VMD.
Maybe the commands I have used are incomplete to make the correct
transformation
from pdb to psf file.

a lot of thanks,

David L. Azevedo

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