VMD-L Mailing List

From: Shirley Li (li19104_at_yahoo.com)
Date: Tue Aug 10 2004 - 13:50:12 CDT

Hi John, Thank you for your message. I sourced the file, then typed the command:
              animatedcds 1 3 "dyn%d.dcd",
but I got the following message:
&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
    Illegal molecule specification 'dyn2.dcd': Could not find molecule 'dyn2.dcd'.mol
    addfile operates on one molecule only
&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
So, it seems that only one dcd file read. I wonder how to fix it. (I have all my dyn1~3.dcd files in the same directory as the script).
 
BTW, I remember that a PSF file has to be read in before loading the .dcd files. Is it right? How to APPEND thse .dcd files to the molecule defined by the PSF file instead of import them as NEW molecule?
 
Thank you again for your help and precious time.
 
Shirley

John Stone <johns_at_ks.uiuc.edu> wrote:
Shirley,
You must remember to "source" the script before you try to run it.
The 50 DCD files must be in the same directory, and in order for the script
to work, you must first "cd" to that directory before you run it.

John

On Tue, Aug 10, 2004 at 09:27:01AM -0700, Shirley Li wrote:
> Thanks so much for your prompt response, John. As you suggested, I changed every occurrence of pdb/PDB into dcd/DCD, and the name into animatedcds.tcl. I saved this script file on my desktop, since I start up VMD(shortcut) from desktop. While I got error message
> "invalid command name 'animatedcds'"
> when I typed the command
> "animatedcds 1 50 "%d.dcd"
>
> What could be the problem? BTW, should I put my fifty *.dcd file in the same directory as that of the script file?
>
> Many thanks.
>
> Best regards,
>
> Shirley
>
>
>
>
> John Stone wrote:
>
> Hi,
> you supply the parameters on the command line as shown in the
> examples at the top of the script.
> However, you'll also need to change the "mol load pdb" and
> "animate read pdb" commands to load the file as a DCD file instead.
> I'd also suggest renaming the script and procedure name, to avoid
> confusion with the original script in the future.
>
> John
>
> On Tue, Aug 10, 2004 at 08:46:27AM -0700, Shirley Li wrote:
> >
> > Hi Mr. Stone,
> >
> > Thank you so much for your help. How should I supply the values of the three parameters? If my files are dyn1.trj, dyn2.trj, ..., dyn50.trj (all in dcd format), in the scipt you provided, should I replace strings "START/END/FILEFORMAT with "1/50/dcd", or instead I should replace "$START/$END/$FILEFORMAT with "1/50/dcd", or should I supply the three parameters in command line?
> >
> > Your help will be highly appreciated.
> >
> > Regards,
> >
> > Shirley
> >
> >
> >
> > >
> > > > 2) In order to analyze multiple trajectory files, how to import these trj files all at once instead of one by one? Could anybody kindly provide me with a script? My .trj files have names as dyn1.trj, dyn2.trj, dyn3.trj, ..., dyn50.trj, and the name of my PSF file is dyn.psf. Once I have such script, how to apply it?
> > >
> > > You can write a Tcl script that loads structures, or adds trajectories.
> > > A relatively simple script that you can learn from is located here:
> > > http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/
> > >
> > >--
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
> >
> >
> >
> >
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> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 
WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
		
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