VMD-L Mailing List

From: Life Sciences Inc (contact.lifesciences.inc_at_gmail.com)
Date: Tue Jul 14 2015 - 10:27:48 CDT

Jhon stone, thank you I solved the problem 5 days back on my own.... ,

On Tue, Jul 14, 2015 at 5:23 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> 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.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> 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
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>