VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Fri Jun 10 2011 - 04:26:48 CDT

I made my version of bigdcd long ago to fix something, cannot even
remember.

However, I still have to press an enter key after vmd is finished the script
with the bigdcd below .. ?

Maria

On Thu, Jun 9, 2011 at 11:02 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> I see that you're using a different version of the bigdcd script
> than the one that's posted on the web. Most likely that's where the
> problem is:
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jun 08, 2011 at 10:33:23AM +0200, maria goranovic wrote:
> > Ajasja, Using -eofexit or using an exit statement at the end of file
> do
> > not work in this case.A
> >
> > On Tue, Jun 7, 2011 at 4:07 PM, Ajasja LjubetiA:*
> > <ajasja.ljubetic_at_gmail.com> wrote:
> >
> > Sorry, it should be:
> > A vmd -dispdev text -eofexit < input.tcl > output.log
> > Regards,
> > Ajasja
> > On Tue, Jun 7, 2011 at 16:02, Ajasja LjubetiA:*
> > <ajasja.ljubetic_at_gmail.com> wrote:
> >
> > Hi,
> > it depends on how you call it. If you use vmdA -eofexitA -e " "
> then
> > it should exit. You can also just put an exit statement at the
> end.
> > Regards,
> > Ajasja
> > On Tue, Jun 7, 2011 at 11:01, maria goranovic
> > <mariagoranovic_at_gmail.com> wrote:
> >
> > Dear All,
> > I have a vmd script (copied below) which I would expect to exit
> > after finishing, but it does not. Any ideas why? version 1.9,
> linux,
> > amd64
> > mol load gro all.gro
> > source mybigdcd2.tcl
> > # closewater.tcl
> > # Justin Gullingsrud
> > # jgulling_at_mccammon.ucsd.edu
> > # 8 November 2004
> > # This script processes a trajectory to create a new file
> containing
> > just
> > # a selection of atoms and the N closest water to that
> selection.
> > A The N
> > # waters are recomputed for each timestep, and need not be the
> same
> > waters
> > # in each timestep (in fact, they probably will not be); thus it
> is
> > in general
> > # meaningless to analyze the dynamics of individual waters.
> > A However, it
> > # may be useful for analyzing the distribution of waters around
> a
> > relatively
> > # static protein or DNA chain.
> > # usage: closewater <molid> <selection text> <# waters>
> <filename
> > prefix>
> > proc closewater A {i} {
> > A set molid 0
> > A set seltext "protein"
> > A set nwat 2500
> > A set prefix "close"
> > A puts "now working in frame $i"
> > A set numinner 0
> > A set inner [list]
> > A set cut 1
> > A while {1} {
> > A A A set sel [atomselect $molid "name OW and within $cut of
> > ($seltext)"]
> > A A A set outer [$sel list]
> > A A A $sel delete
> > A A A set numouter [llength $outer]
> > A A A if { $numouter < $nwat } {
> > A A A A set inner $outer
> > A A A A set numinner $numouter
> > A A A A incr cut
> > A A A A continue
> > A A A }
> > A A A break
> > A A }
> > A puts "Found $numouter waters at cutoff $cut"
> > A catch { unset ohash }
> > A foreach ind $outer { set ohash($ind) 1 }
> > A foreach ind $inner { unset ohash($ind) }
> > A set outer [lrange [array names ohash] 0 [expr $nwat -
> $numinner -
> > 1]]
> > A set watind [concat $inner $outer]
> > A set sel [atomselect $molid "($seltext) or same residue as
> (index
> > $watind)"]
> > A set j [format %06d $i]
> > A $sel writepdb [format $prefix-$j.pdb]
> > A exec editconf -f $prefix-$j.pdb -o $prefix-$j.gro -resnr 1 &
> > A }
> > bigdcd closewater temp.xtc
> > bigdcd_wait_till_done
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
> 

-- 
Maria G.
Technical University of Denmark
Copenhagen