VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Mar 27 2015 - 12:38:49 CDT

Hi!

You can also do everything from VMD.
Load just the first N frames. Save a pdb of protein only. Save a DCD of
protein only.
delete all frames and load the next N and only the protein to the next DCD
file.
If you only have to load two or three pieces this might be more convenient.

Best regards,
Ajasja

On 27 March 2015 at 17:55, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:

> Hi Jevgenij,
>
> You have to use catdcd for that purpose. The procedure is the following:
>
> 1. Load psf + pdb
> 2. Make a selection: set sel [atomselect top "selection text"]
> 3. Write psf of that: $sel writepsf selection.psf
> 4. Write indices of the selection:
> set ch [open indices.txt w]
> puts $ch [$sel list]; # [$sel list] is same as [$sel get index]
> close $ch
> 5. Use catdcd to extract your selection from the trajectory:
> catdcd -o output_file.dcd -otype dcd -i indices.txt trajectory_file
>
> Good luck,
> Maxim
>
> > On Mar 27, 2015, at 11:43 AM, Jevgenij Raskatov <jraskato_at_ucsc.edu>
> wrote:
> >
> > Dear users, I am loading a large simulation of a protein in a waterbox
> into vmd, and would like to only load the protein portion, because
> otherwise my computer crashes. I understand that one can display the
> protein only portion, but how about editing it prior to loading, so as to
> maximize performance?
> >
> > Thanks
> >
> > --
> > Dr. Jevgenij A. Raskatov
> > Assistant Professor in Chemistry and Biochemistry
> >
> > Tel.: +1-831-459-2978
> >
> > Department of Chemistry and Biochemistry
> > Physical Science Building 356
> > 1156 High Street
> > Santa Cruz, CA
> > 95064 USA
>
>
>