VMD-L Mailing List

From: Jesper Soerensen (lists_at_jsx.dk)
Date: Mon Oct 10 2011 - 12:42:30 CDT

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

Is this a bug in the pqr plugin?

Best regards,
Jesper