VMD-L Mailing List

From: Anthony Cruz Balberdi (anthony.cruz5_at_upr.edu)
Date: Tue Apr 09 2013 - 10:00:24 CDT

Hi:

You should use bigdcd (
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/ ). You
could do a script that do exactly that and without memory problem since
bigdcd load one frame at a time (Check the examples). If you need help let
me know...

Best Regards,

Anthony

On Mon, Apr 8, 2013 at 7:42 PM, Yarrow Madrona <amadrona_at_uci.edu> wrote:

> Hello,
>
> I am trying to convert a dcd to a series of pdb's without opening the VMD
> GUI. The reason is that I don't have enough ram to store the DCD (70,000
> frames) into memory. VMD always crashes unless I use a truncated DCD. I
> would like to use all frames since the frames will be analyzed by another
> software (Caver3.0). Is there a way to tell vmd to write out all PDBs in
> the command line (preferably without water although I can remove those
> later)?
>
> Thank you
>
>
> --
> Yarrow Madrona
>
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
>
>
>
>