VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Wed Oct 25 2006 - 19:33:52 CDT

Hi,
I have done this kind of thing (making a cubical box out of a pdb for a
single molecule). You do it 'manually' by a) translate in another direction,
b) write out a pdb file, c) concatenate new and old files. You can go from 1
-> 4 -> 16 molecules, etc. This example will give you the idea:
Note: Make sure to remove the 'END' line at each concatenation.

set sys [mol new fixed.pdb]
set all [atomselect $sys all]
set a [molinfo top get a]
set b [molinfo top get b]
# Measure the center
set com [measure center $all]
$all moveby [vecscale -1]

# Write out the first system
$all writepdb sys1.pdb

# Translate by +x and write out new config
$all moveby [list $a 0 0]
$all writepdb sys2.pdb

# Translate by -x and +y and write out new config
$all moveby [list [expr {-1*$a}] 0 0]
$all moveby [list 0 $b 0]
$all writepdb sys3.pdb

# Translate by +x and write out new config
$all moveby [list $a 0 0]
$all writepdb sys4.pdb

> On Tue, Oct 24, 2006 at 06:08:56PM +0200, Javaria Ahmed wrote:
> > I have a pdb file, for inorganic crystal structure. It has 14 atoms. I
> want
> > to draw a bigger structure, as big as, with lets say 500 / 1000 atoms.
> How
> > would I do that using VMD and get the pdb file for that structure.
> >
> > I tried doing that by drawing periodic images.But I dont know how to
> save
> > the coordinates in pdb file.
> >
> > Regards
> >
> > Javaria
>
> --
****************************************
Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
USA
Phone: 1-949-824 9921
email: sengupta_at_uci.edu
****************************************