Re: query about wrapped coordinates

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Tue May 08 2007 - 13:37:53 CDT

What does it mean your protein goes in and out? Does it re-enter the box
from the other side?

Gianluca

On Tue, 8 May 2007, hl332_at_drexel.edu wrote:

> Hi,

> Thanks again for your useful suggestions. First of all, I am sorry to
> bother you again for problem. I did what you and Gianluca suggested but
> still have two caveats. Here they are: a. I have to run following
> commands 2 times in tcl console in the order below in order to make the
> unwrap work. The commands are:
>
> source unitcell.tcl #cell dimen. for all frames
> source unwrap.tcl
> unwrap protein
>
> these three commands need always to be run twice. The first time i run
> it prints same error line (box small...) from unwrap script but when i
> repeat them again in same console, i can see protein unwrapped. I am not
> sure why it is happening?
>
> b. Second problem is that although after running twice above commands,
> it unwraps my selection but just after that when i try moving along
> trajectory again, i can observe selection going in/out. Although,
> towards the last frame, i can see whole protein unwrapped on one side. I
> dont understand why it happens. My purpose is to calculate COM position
> of my protein at each time frame and until i can see protein unwrapped
> at each frame, I am not sure the coordinated I am printing are correct
> or not?
>
> PLease help me to get out of this 'stuck' situation.
>
>
> Regards
> Harish
>
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823
>
> ----- Original Message -----
> From: Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar>
> Date: Tuesday, May 8, 2007 9:46 am
> Subject: Re: namd-l: query about wrapped coordinates
>
> > If you look once again at molinfo documentation you will notice
> > that you
> > only set a b c for the current frame. For a trajectory you should
> > use a
> > loop as suggested by gianluca.
> >
> > hl332_at_drexel.edu escribió:
> > > 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.
> > >> -----------------------------------------------------
> > >>
> > >
> > >
> > >
> > >
> >
> >
>
>

-----------------------------------------------------
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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