From: John Stone (
Date: Tue Jul 14 2015 - 10:23:36 CDT

  You didn't show what you did to run catdcd, so it's hard to say what went
wrong. When asking questions about why scripts don't run, you need to provide
all of the steps you performed. Nobody can guess what you might have done
wrong if you don't show us what was done.

  John Stone

On Wed, Jul 08, 2015 at 06:59:30PM +0200, Life Sciences Inc wrote:
> Hi all
> I am trying to strip water and ions from my trajectory file so that I can
> only have my molecule of interest in trajectory file.
> I striped water first by using the following commands
> set sel [atomselect top "not water"]
> set out [open "indices_nowater.txt" w]
> puts $out "[$sel list]"
> close $out
> $sel writepsf abc.psf
> and got the psf file and now I am trying to strip ions from the same psf
> file and want to write the new onw with the same commands
> set sel [atomselect top "ions"]
> set out [open "indices_ions.txt" w]
> puts $out "[$sel list]"
> close $out
> $sel writepsf new_abc.psf
> then from this psf I will use catdcd to generate dcd files.
> but I am getting an error on writing the psf "atomsel: frame -1 out of
> range for molecule 0", how to correct this or if someone can have better
> script to strip water and ions from psf file and to write the new one.. or
> something like that.
> I would be really thankful to you all

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349