From: Axel Kohlmeyer (
Date: Sun Feb 28 2016 - 11:48:58 CST

On Sun, Feb 28, 2016 at 6:16 PM, zeynab hoseyni <> wrote:
> Dear all,
> I have a carbon nanotube pdb file and I created the related psf file like
> following:
> After loading the pdb file in vmd I tried following:
> set sel [atomselect top all]
> $sel writepdb semi-conductor_cnt.pdb
> $sel writepsf semi-conductor_cnt.psf
> This procedure goes ahead with no error, but then when I try to solvate

there is no error message, but there are serious problems.
a pdb file does not contain all the information required for a
complete psf file, especially not a psf suitable for simulations.
VMD will use the information present, use heuristics for a few more,
but skip over what is not there or use zeros or empty strings.


> the nano-tube, like following:
> package require solvate
> solvate semi-conductor_cnt.psf semi-conductor_cnt.pdb -t 10 -o
> semi-cond-solv
> I received this error:
> Info) generating solute plus one replica of water...
> psfgen) reading structure from psf file semi-conductor_cnt.psf
> psfgen) error reading atoms from psf file
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> When I looked into the error written in the vmd environment I see this
> error:
> PSF file is in CHARMM format; XPLOR format required.
> I thought when I use writepsf command it makes the psf file in the xplor
> format but seems I was wrong..
> Can anybody help on this?
> Thanks,
> Zeynab

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.