Re: query about wrapped coordinates

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Fri May 04 2007 - 17:53:42 CDT

This script needs the information about the box size. Usually, this is
written in the dcd file if you specified "DCDUnitCell yes" in your NAMD
config file. If you didn't specify "DCDUnitCell yes" then the information
about the box size cannot be retrieved from your DCD file. But this should
not be a big deal because you were running your simulation at constant
volume. In this case you can try have VMD read a pdb file which contains
the crystal information in the first line, e.g.:

CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1
...

You have to replace "50.000 50.000 50.000" by the x-y-z dimensions of
your box and have VMD read it before it reads the DCD.

I hope this helps,

                Gianluca

On Fri, 4 May 2007, hl332_at_drexel.edu wrote:

> Hi Dr. Gianluca,

> I tried the script provided by you but when I am trying to run the
> command "unwrap protein" after sourcing the script, it gives one error:
> Box abnormally small or no box size info available
>
> I also did not understand the limitation of script given on its introduction page. Can you help me??
>
> Regards and Thanks
> Harish
>
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823
>
> ----- Original Message -----
> From: Gianluca Interlandi <gianluca_at_u.washington.edu>
> Date: Friday, May 4, 2007 3:54 pm
> Subject: Re: namd-l: query about wrapped coordinates
>
> > > I have been doing a periodic NVE run of my protein in
> > solvent.> I had the "wrap all" command on during the run. Some part
> > of my protein
> > > which moved out of box has been wrapped back but i want to know the
> > > coordinates of my protein corresponding to the one when it was
> > moving in
> > > one direction. I also want to fit the different frames to first
> > one in
> > > such a way that i dont observe the half portion of protein moving on
> > > other side. ANy suggestion are highly appreciated from more
> > experienced> users.
> >
> > Hi Harish,
> >
> > I forward you here the response I got from Jerome when I posted the
> > same
> > question on the NAMD list a year ago.
> >
> > Best,
> >
> > Gianluca
> >
> > ---------- Forwarded message ----------
> > Date: Thu, 5 Oct 2006 23:08:18 -0400
> > From: Jerome Henin <jhenin_at_vitae.cmm.upenn.edu>
> > To: Gianluca Interlandi <gianluca_at_u.washington.edu>
> > Cc: <namd-l_at_ks.uiuc.edu>
> > Subject: Re: namd-l: "wrapAll on" with a complex
> >
> > Gianluca:
> > Using VMD with the attached script should solve that. Just source
> > the Tcl file
> > and use the 'unwrap' procedure.
> > Best,
> > Jerome
> >
> > Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit :
> > > I am performing a simulation of a complex consisting of two
> > proteins. I am
> > > using the option "wrapAll on". One of the two proteins has
> > reached one of
> > > the boundaries of the box and it has been wrapped around. The other
> > > protein is still in the same position.
> > >
> > > Is there a way to "recover" from the wrapping a posteriori, i.e.,
> > to bring
> > > the protein back to its original image?
> > >
> > > Thanks a lot,
> > >
> > > Gianluca
> > >
> > > -----------------------------------------------------
> > > Dr. Gianluca Interlandi gianluca_at_u.washington.edu
> > > +1 (206) 685 4435
> > > +1 (206) 714 4303
> > > http://biocroma.unizh.ch/gianluca/
> > >
> > > Postdoc at the Department of Bioengineering
> > > at the University of Washington, Seattle WA U.S.A.
> > > -----------------------------------------------------
>
>

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
                    +1 (206) 685 4435
                    +1 (206) 714 4303
                    http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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