VMD-L Mailing List

From: David L. Azevedo (david888_at_uol.com.br)
Date: Fri Sep 24 2004 - 08:52:13 CDT

I am trying to learn how to use NAMD and VMD. I have got the
'Simulation of water permeation through nanotubes' tutorial files and
I´ve tried
to generate the nanotubes.psf file from the nanotubes.pdb file. Using
some sort
of commands like this:

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

And I obtain many warnings 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 'pdbf file' and try to do other kinds of simulations.
Maybe the commands I have used are incomplete to do the correct translation

a lot of thanks,

David L. Azevedo