Re: query about wrapped coordinates

From: hl332_at_drexel.edu
Date: Mon May 07 2007 - 19:05:40 CDT

Hi Dr. Gianluca and Cesar,
  Thanks for this information. I took value of a,b,c from the .xst file of my run and loaded the trajectory as usual, then used the molinfo commands for setting a,b,c values. Sourcing the script and applying command unwrap protein again gives the error:
" Box abnormally small or no box size info available"
For a moment i see the protein inside the box but when i slide the frames, the situation is same, i can see it going in/out. Please suggest what might be wrong with the way I am doing.
  Thanks again.

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: Monday, May 7, 2007 7:26 pm
Subject: Re: namd-l: query about wrapped coordinates

> I have actually found a much easier way of adding the crystal
> information
> to your trajectory.
>
> Forget about creating a pdb file. You simply load your trajectory
> into VMD
> the way you have always done it. Now you use the command molinfo to
> add
> the crystal information:
>
> Open a TK console: Extension -> TK console
>
> Assuming you have used a cubic box of side length 50 type the
> following:
> molinfo top set a 50
> molinfo top set b 50
> molinfo top set c 50
>
> This should be enough. Now run the unwrap script.
>
> Gianluca
>
> On Mon, 7 May 2007, Gianluca Interlandi wrote:
>
> > > Should I construct A PDB FILE in the fashion you said or should
> i
> > > save this from end of my dcd file using .coor file or how.
> where exactly
> > > should i given the unit cell coordinates?
> >
> > It doesn't matter which pdb file you use. You can for example
> write out
> > the first frame of your simulation as a pdb file (.pdb
> extension). Call it
> > first.pdb. Then you open the file first.pdb in a text editor
> (nedit or
> > emacs in linux or wordpad in windows). Now you will see that the
> first
> > line of that file is:
> >
> > CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1
> 1
> >
> > This is the crystal information. The first three numbers are the
> dimension
> > of the cell. You have to replace "0.000 0.000 0.000" with the
> dimensions
> > of the box you have used. When you do that make sure that the "."
> is
> > always at the same position. You can figure out the dimension of
> your box
> > also from the last .xsc file written. Save your file first.pdb.
> Now open a
> > new VMD and load the file first.pdb and then your trajectory.
> Apply the
> > unwrap script.
> >
> > There might be more elegant solutions but I hope this one helps,
> >
> > Gianluca
> >
> >
> > I am sorry for this trouble
> > > but if you can elaborate a more, it will solve my problem.
> Thanks n
> > > regards
> >
> > > 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 6:53 pm
> > > Subject: Re: namd-l: query about wrapped coordinates
> > >
> > > > 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.
> > > > -----------------------------------------------------
> > >
> > >
> >
> > -----------------------------------------------------
> > 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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