Re: query about wrapped coordinates

From: hl332_at_drexel.edu
Date: Mon May 07 2007 - 16:09:07 CDT

Hi Dr. Gianluca,
   I tried it but could not make it work. I dont have this information for sure in my dcd file. I didnt really understand the pdb stuff you said. 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? 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.
> -----------------------------------------------------

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