VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 29 2004 - 13:20:48 CDT

The PBCWrap script doesn't attempt to keep bonded atoms
together when it wraps them, whereas the built-in wrap code
in NAMD does do this. You could fix this by modifying the
script to either disconnect affected bonds (bonds greater than
a particular length), or you could draw your structure with the
"dynamic bonds" representation (which does this already), or
you could teach the script to wrap connected atoms as a unit
(all or nothing) rather than individually. There are advantages
and disadvantages to each strategy, it'll depend a lot on the
particular structure you're working with and what sort of
wrapped result your looking for.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 28, 2004 at 08:03:45PM -0700, Vani Krishna wrote:
> John:
>
> i tried using the script but there are some problems.
>
> the coordinates in this case are wrapped such that
> there are these weird bonds going across the box. if i
> just run for a few steps in NAMD with 'wrapAll' turned
> on, there is wrapping, but no weird bonds across the
> box. I don't know what is the difference between the
> two wrappings
>
> any suggestions?
> Thanks
> Vani
>
> --- John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Assuming you're using NAMD and you have the
> > appropriate .xst files,
> > then this script may do what you're asking for:
> >
> >
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/pbcwrap/
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
>
>
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078