VMD-L Mailing List

From: Jeremiah Babcock (zhc605_at_my.utsa.edu)
Date: Wed Jun 25 2014 - 19:07:37 CDT

Hi Puspita,
      Not sure if you did this but if you just need the secondary structure
of the protein you could strip out the solvent molecules. That would really
help on the file size. Also, which OS version are you using?

Regards,
Jeremiah Babcock

On Wed, Jun 25, 2014 at 8:23 AM, Puspita Halder <puspitah_at_gmail.com> wrote:

> Dear VMD users,
>
> I need to generate the secondary structure of my protein from a 50 ns
> simulation run. I used sscache earlier for 2-4 ns simulations of the
> protein. Now the file sizes are huge (~ 50 GB) so I assume that I cannot
> directly use sscache. I tried to combine sscache with bigdcd.tcl script but
> failed to do so. Please help me with your valuable suggestions regarding
> this. Is there any ready script available ?
>
> Thanks
> Puspita
>