From: zeynab hoseyni (zmhoseyni_at_gmail.com)
Date: Sun Feb 28 2016 - 13:22:47 CST

Hi axel,

Thanks for your guide. I discovered something wrong in my pdb file
and corrected it. Now everything is fine.

Thanks a lot,
All the Best,
Zeynab

On Sun, Feb 28, 2016 at 5:48 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sun, Feb 28, 2016 at 6:16 PM, zeynab hoseyni <zmhoseyni_at_gmail.com>
> 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.
>
> axel.
>
>
> > 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 akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>