Hi John,
Thanks for that reply. As you can see I have cross-posted this on the
AMBER mailing list to see if anyone would be willing to help with that.
I would do it, but I do not have enough experience with AMBER to do so.
I know the AMBER program "ambpdb" can do this, but it would be a neat
feature to have accessible in VMD.
Best regards,
Jesper
On Oct 13, 2011 17:25 "John Stone" <johns.ks.uiuc.edu>
<johns.ks.uiuc.edu> wrote:
> 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.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.gmail.com>
> > <akohlmey.gmail.com> wrote:
> >
> > hi jesper,
> >
> > On Mon, Oct 10, 2011 at 1:42 PM, Jesper Soerensen <lists.jsx.dk>
> > <lists.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
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Received on Mon Oct 17 2011 - 17:00:02 PDT
