VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat May 13 2006 - 18:11:27 CDT

On Sat, 13 May 2006, TZU-LAN YEH wrote:

> moveframes top "protein"
> set $sel [atomselect top "water"]
> pbcwrap $sel
>
> and then it prompted:
> expected integer but got "atomselect3"
>
> Did I misuse the pbcwrap?

please check whether the definition of the
pbswrap procedure matches the documentation.

if you are using 'moveframes' which is a hacked
version of 'fitframes' you have most likely
a hacked version of pbcwrap that takes the box
information from the .dcd file (if present).

for that to work you have to add a

animate delete all

after loading the molecule (in case it is not a .psf file).
if your .dcd file does not contain the box information
you may have to add this manually or using a script:
http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect6
note that this works only for constant volume simulations...

>
> Also, I've tried not to specify anything and vmd gave me really weird
> things. I can see two very dense water layers (I think that's what the
> script wrap) and while the animation went, the protein still left the box.
> (Any idea why this does not work?) So I thought I might misused it and tried

i suggest you pick a short part of the trajectory and verify
that each of the various steps work and if you have doubts,
feel free to upload your data and scripts to the public VMD
biofs area, so we can have a closer look at it.

best regards,
   axel.

> to wrap some water molecules.
> According to the documentation within the script:
>
> #
> pbcwrap
>
> #
> ------------
>
> # Wraps atoms of selection $sel around PBC unit cell
> boundaries.
> # Unit cell geometry is read from the xst-file $xst.
>
> Usage:
>
> # pbcwrap selection xstfile [beg $first] [end $last] [firsttime
> $firsttime]
> # [delta $delta] [outfile $outfile]
> #
>
> #
> Example:
>
> # set sel [atomselect top "segname
> OXY"]
> # pbcwrap $sel mysimulation.xst beg 100 end 200 firsttime 50000 delta
> 1000
>
>
> Thank you.
>
> On 5/10/06, Guo Zhi <gzgzgz_at_gmail.com> wrote:
> >
> > I strongly recommend you use the pbcwrap plugin written by Dr. Jan Saam.
> > you can find this plugin in VMD-L thread by searching keyword "pbcwrap
> > fitframes", a specific usage was given by Alex. Try it.
> >
> >
> > 2006/5/10, TZU-LAN YEH <tzulan.yeh_at_gmail.com>:
> >
> > > Dear VMD users,
> > >
> > > I want to monitor water around a certain residue, but my protein is
> > > drifting out of the water box. When I used the selection "water and within *
> > > of resid # ", VMD showed the water molecules within the distance, but only
> > > those inside the box. When I turn on peridoic cell in the diection protein
> > > drifting, VMD still wouldn't show those water molecules. Neither did they
> > > appear on the other side of the water box. Could someone give me some
> > > advises how to solve this problem?
> > >
> > > Thank you in advance.
> > >
> > > Tzu-Lan
> > >
> >
> >
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.