Re: query about wrapped coordinates

From: hl332_at_drexel.edu
Date: Tue May 08 2007 - 13:15:34 CDT

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.
> >> -----------------------------------------------------
> >>
> >
> >
> >
> >
>
>

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