VMD-L Mailing List

From: Viswanadham Sridhara (muta.mestri_at_gmail.com)
Date: Thu Sep 08 2005 - 10:59:27 CDT

Thanks, John.
Appreciate your patience.
 Best Regards,
Viswam.

 On 9/8/05, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> 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
> 

-- 
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University, "VIRGINIA".