VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 19 2007 - 11:01:24 CDT

Hi,
  You haven't provided quite enough information to determine what is
causing your problem. Can you send me the verbatim source code of your
script and also the exact sequence of commands you're using to run it?
Are you running the script interactively, or are you running it in batch
mode by redirecting VMD's input/output, or with -e?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 19, 2007 at 10:03:24AM -0400, Vishal Kopardé wrote:
> Hello,
> I am having a very weird problem with bigdcd, that the number of
> frames accessed is equal to the number of new line characters following
> the bigdcd statement. How do I get over it? I have 5000 frames in my dcd
> file and right now I am adding 5000 blank lines after the bigdcd
> statement in the tcl file.
> This problem was reported earlier but I could not find a
> straightforward solution.
>
> tcl script
> **********************
> source bigdcd.tcl
>
> proc zeros {num} {
> set list1 {}
> for {set i 0} {$i<$num} {incr i} {
> lappend list1 0
> }
> return $list1
> }
>
> proc sumlists {list1 list2} {
> if {[llength $list1] != [llength $list2] } {
> echo " ERROR lists are unequal "
> return
> }
> set list3 {}
> foreach i $list1 j $list2 {
> lappend list3 [expr $i + $j]
> }
> return $list3
> }
>
> set psffile hex.psf
> set dcdfile prod1.dcd
> set hblength 3.50
> set rshell 4.0
> set hbangle 30
>
> set res {}
> for {set k 1} {$k <=21} {incr k} {
> lappend res $k
> set f2 [open ${k}pmol1.dat w]
> close $f2
> unset f2
> set f2 [open ${k}pmol2.dat w]
> close $f2
> unset f2
> set f2 [open ${k}pmol1num.dat w]
> close $f2
> unset f2
> set f2 [open ${k}pmol2num.dat w]
> close $f2
> unset f2
> }
> set res1 {}
> for {set j 1} {$j <=30} {incr j} {
> set k [expr $j+21]
> lappend res1 $j
> set f2 [open ${k}pmol1.dat w]
> close $f2
> unset f2
> set f2 [open ${k}pmol2.dat w]
> close $f2
> unset f2
> set f2 [open ${k}pmol1num.dat w]
> close $f2
> unset f2
> set f2 [open ${k}pmol2num.dat w]
> close $f2
> unset f2
> }
>
> proc doit { i } {
> global res res1 hblength hbangle rshell
> **********
> STATEMENTS
> ************
> }
>
>
> mol delete all
> mol load psf $psffile
> bigdcd doit $dcdfile
>
> 5000 blank lines here
> ************
>
>
> Your help is greatly appreciated.
> Thank you,
> Vishal
>
> --
> Vishal N Kopardé, Ph.D.
> http://www.people.vcu.edu/~vnkoparde/ 

-- 
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