From: John Stone (
Date: Fri May 16 2014 - 10:15:20 CDT

What operating system are you running? This sounds like something
that might occur on MS Windows when files are opened as text rather than
binary, for example. It does seem like you're closing the file properly which
would be the usual cause of truncation, so this leaves OS-specific causes
as my best guess at the moment.

  John Stone

On Thu, May 15, 2014 at 03:13:58PM -0400, Karl Lundquist wrote:
> Hi all,A
> I am attempting to make an index file to use with catdcd to wrote only
> certain atoms to my dcd files. Below is a copy of my script:A
> package require psfgen
> set infile ../2014-5-01-run/ionizedkcl
> set seltext "(resname AHEP AGLC AKDO AGAL or (chain L and name N P O11 O12
> O13 O14 C11 C12 HN1 HN2 HN3 H11A H11B H12A H12B))"
> set newpsf headsonly
> readpsf $infile.psf
> coordpdb $infile.pdb
> mol load psf $infile.psf pdb $infile.pdb
> set all [atomselect top "all"]
> set sel1 [atomselect top $seltext]
> set selnot [atomselect top "not $seltext"]
> set indices [$sel1 get index]
> set file [open findexfile.ind w]
> foreach var $indices {
> A A A puts $file $var
> }
> flush $file
> close $file
> foreach segid [$selnot get segid] resid [$selnot get resid] atomname
> [$selnot get name]
> {
> A A A delatom $segid $resid $atomname
> }
> writepsf $newpsf.psf
> exit
> The problem I'm having is that not all of the indices are printed to
> findexfile.ind. It gets cut off after the first 6000 or so entries.
> However, when I put these commands line by line into the VMD tkconsole,
> the command "puts $indices" prints them all without any issue. Anyone have
> any insight as to why this might be happening?
> Thanks,
> Karl

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