VMD-L Mailing List

From: TZU-LAN YEH (tzulan.yeh_at_gmail.com)
Date: Sat May 13 2006 - 11:04:20 CDT

Hi all,

Thanks for the suggestions. I've downloaded the pbcwrap and moveframes
scripts, but it didn't work.

Here's how I did it.

load the molecule
load the dcd file

source moveframes.tcl
source pbcwrap.tcl

moveframes top "protein"
set $sel [atomselect top "water"]
pbcwrap $sel

and then it prompted:
expected integer but got "atomselect3"

Did I misuse the pbcwrap?

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
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
> >
>
>