VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Fri Jun 10 2011 - 04:36:02 CDT

PS: but if I redirect the output and error using : vmd -dispdev text
-eofexit < temp.tcl > temp.out 2> temp-error.out

then the extra return key is not needed. Although this works, I cannot see
why redirection sorts out the problem.

On Fri, Jun 10, 2011 at 11:26 AM, maria goranovic
<mariagoranovic_at_gmail.com>wrote:

> 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
> 

-- 
Maria G.
Technical University of Denmark
Copenhagen