From: Jesper Soerensen (lists_at_jsx.dk)
Date: Mon Oct 10 2011 - 15:41:54 CDT

Hi Axel,

>those are not the radii from the amber prmtop file,
>but whatever VMD has guessed based on what it
>had as information about the element.

>that is why it doesn't flag those radii as being
>present when writing the pqr file.

That makes more sense then I guess. Is there a way to extract the prmtop
radii using VMD then?
Also, just to make sure, are the charges that it exports from the prmtop
file then?

Best,
Jesper

On Oct 10, 2011 20:40 "Axel Kohlmeyer" <akohlmey_at_gmail.com>
<akohlmey_at_gmail.com> wrote:

> hi jesper,
>
> On Mon, Oct 10, 2011 at 1:42 PM, Jesper Soerensen <lists_at_jsx.dk>
> <lists_at_jsx.dk> wrote:
> > Hi all,
> >
> > From an amber force field simulation I would like to output a few
> > frames
> > into .pqr files using the animate write command, but I get an error
> > regarding the atomic radii.
> >
> > I have loaded in a prmtop (topology file) and a single snapshot (for
> > testing). I use the command:
> > > animate write pqr test.pqr beg 0 end 0 skip 1 0
> >
> > I then get the following error:
> > > pqrplugin) Warning no atom radii available, assigning radii of 1.0
> >
> > The charges look correct, but all the radii are set to 1.0, which is
> > of
> > course wrong. The atomic radii specifications should be present in
> > the
> > prmtop file - and in fact I can output these manually by
> > > set sel [atomselect top "protein"]
> > > $sel get radius
>
> those are not the radii from the amber prmtop file,
> but whatever VMD has guessed based on what it
> had as information about the element.
>
> that is why it doesn't flag those radii as being
> present when writing the pqr file.
>
> cheers,
> axel.
>
> >
> > Is this a bug in the pqr plugin?
> >
> > Best regards,
> > Jesper
> >
> >
> >
>
>
>