VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 10 2011 - 13:40:51 CDT

hi jesper,

On Mon, Oct 10, 2011 at 1:42 PM, Jesper Soerensen <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
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.