VMD-L Mailing List

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Wed Jun 07 2006 - 12:24:03 CDT

That does the trick. Thank you very much!

Gustavo.

On 6/7/06, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> This sort of thing can be done by running VMD in text mode if you like:
> http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/ug/node192.html
>
> vmd -dispdev text -eofexit < input.tcl > output.log
>
> In your script, you'd do something like:
>
> mol new myfile.parm7
> mol addfile myrestart.rst7
> set sel [atomselect top "same residue as within 3 of chain X"]
> set outfile [open "myresidues.txt" w]
> puts $outfile [lsort -unique [$sel get resid]]
> close $outfile
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Wed, Jun 07, 2006 at 11:56:02AM -0400, Gustavo Seabra wrote:
> > Hi,
> >
> > I was wondering if any of you experts could help me with a simple command.
> >
> > I'd like to be able to get, from an Amber restart file, all the waters
> > within a distance (say, 3A) from a central molecule. I know how to do
> > thins in the GUI, byt using, for example, "same residue as within..."
> > .But, ideally, I want to do this without raising the whole VMD: maybe
> > just a shell script or even a one liner that can print out the residue
> > numbers to a separate file. Is that possible?
> >
> > Thanks.
> >
> > --
> > ---------------------------------------------------------------------------------------------
> > Gustavo Seabra Postdoctoral Associate
> > Quantum Theory Project University of Florida
> > Registered Linux user number 381680
> > Say NO! to software patents: http://www.nosoftwarepatents.com
> > ---------------------------------------------------------------------------------------------
> > If at first you don't succeed...
> > ...skydiving is not for you.
>
> --
> 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
>