VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 09 2011 - 16:02:54 CDT

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