VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 13 2011 - 10:25:45 CDT

Hi,
  Yes, the "parm7" plugin reads the charges and masses and various
name information, but ignores the radii information in the file.
I seem to vaguely recall this is because the radii are stored with
some sort of scaling operation applied in some case and not being
AMBER experts it was safer not to try and use it than to use it and
get it wrong. If someone with more experience with AMBER wants to
have a look, it should be trivial to make the parm7 plugin read radii
information when it is available.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Oct 10, 2011 at 10:41:54PM +0200, Jesper Soerensen wrote:
> 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> wrote:
>
> 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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