VMD-L Mailing List

From: Yunjie Zhao (yjzhao.wh_at_gmail.com)
Date: Wed Sep 18 2013 - 08:30:59 CDT

Hi,

Thanks for the quick reply. How to provide the suitable topology file
matched with the force field? The pdb file does not have any hydrogens when
I am doing the Automatic PSF Builder. I want to generate the psf file with
the atoms exactly as the input pdb file. Could you please tell me how to
do this with more details? Thanks a lot.

Regards,
Yunjie

On Wed, Sep 18, 2013 at 4:22 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Sep 18, 2013 at 8:57 AM, Yunjie Zhao <yjzhao.wh_at_gmail.com> wrote:
> > Hi,
> >
> > I have generate a psf file from the pdb structure using Automatic PSF
> > Builder in VMD. However, it adds the hydrogen atoms as well. I want to
> > remove all the hydrogen atoms from the generated psf file.
>
> yes, it will generate a psf file according to the topology file that
> you provide. that is how this works. if you want to have autopsf to
> not generate these, you need to supply a suitable topology file. this
> has to match your force field as well. if you simply strip off the
> hydrogens, you will have thoroughly inconsistent parameters assigned
> to your atoms.
>
> axel.
>
>
>
> > I am trying to use psfgen.
> > resetpsf
> > readpsf myfile.psf
> > coordpdb myfile.pdb
> > mol load psf myfile.psf pdb myfile.pdb
> > set bad [atomselect top "hydrogen"]
> > foreach segid [$bad get segid] resid [$bad get resid] name [$bad get
> name]
> > {delatom $segid $resid $name}
> >
> > But, this does not work.
> >
> > What's wrong with this? Thanks for any help and explanation.
> >
> > Regards,
> > Yunjie
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
> 

-- 
Yunjie Zhao, PhD
Department of Physics
The George Washington University