VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 08 2005 - 10:54:50 CDT

Hi,
  You can use something simple like this:

  set f [open "foo.dat" w]
  set sel [atomselect top "water and exwithin 3 of protein"]
  set residlist [lsort -unique -integer [$sel get resid]]
  foreach idx $residlist {
    puts $f "$idx"
  }
  close $f

On Thu, Sep 08, 2005 at 11:44:29AM -0400, Viswanadham Sridhara wrote:
> Hi John,
> Thanks for the quick reply.
> I understood the commands you gave.
> But my problem is I cannot write them to a file. If its the case of pdb,
> writepdb command directly creates a .pdb file in the working directory, but
> I am unable to find a simple way to write "array" into a file. I know its a
> very simple question, but still I am having problems with this, as I am new
> to Tcl Scripting.
> Thanks in advance.
> -Viswam
>
> On 9/8/05, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >
> > Hi,
> > I'd suggest modifying the selection so that you're just selecting
> > the waters, and and then query the resids and sort unique. Something
> > like this:
> > set sel [atomselect top "water and exwithin 3 of protein"]
> > set residlist [lsort -unique [$sel get resid]]
> >
> > From there you can write the contents of $residlist to a file if you wish.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Sep 08, 2005 at 11:29:54AM -0400, VISWANADHA SRIDHARA wrote:
> > > Hi VMD users,
> > >
> > > I am trying to get the resid's of the molecules in a trajectory.
> > >
> > > The script I wrote I have seen in VMD tutorial is
> > >
> > > set number_frames [molinfo top get numframes]
> > > set selection [atomselect top "exwithin 3 of protein"]
> > > for {set i 0} {$i < $number_frames} {incr i} {
> > > $selection frame $i
> > > $selection update
> > > $selection writepdb water_$i.pdb
> > > }
> > >
> > > Now I want to find the residue ID's of the water molecules in
> > water_$i.pdb
> > > files.
> > > Is there any straight coding which can be incorporated in the script to
> > > directly get residue ID's in a notepad/wordpad file.
> > > I can use gromacs or other tool to convert each water_$i.pdb file to
> > > water_$i.ndx file, but can I use "$selection get index" and then store
> > that
> > > in a file(ofcourse not pdb).
> > >
> > > Thanks in advance and Best Regards,
> > > Viswam.
> >
> > --
> > 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
> >
>
>
>
> --
> Viswanadham Sridhara,
> Graduate Research Assistant,
> Old Dominion University, "VIRGINIA". 

-- 
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