From: Thomas Bishop (
Date: Mon Dec 05 2011 - 08:54:11 CST

Here's a script I put in my ~/bin directory.
I called it ~/bin/dcd2pdb.vmd

to make a bunch of numbered xyz files all I do is

vmd -parm7 some.parm -dcd some.dcd -e ~/bin/dcd2pdb.vmd
vmd -psf some.psf -dcd some.dcd -e ~/bin/dcd2pdb.vmd
vmd -mol2 some.mol2 -dcd some.dcd -e ~/bin/dcd2pdb.vmd

I structure many of my scripts this way....
leave the inputs as command line arguments so that I can apply the
script (which is typically some sort of analysis ) to
any trajectory.

This script was originally used to make pdb files that I sent to 3DNA or
curves for DNA helical parameters analysis.
I found that on some computers, I could write the pdb, analyze it and
remove very quickly b/c the OS cached the
write/read/delete operations and the file was deleted before ever being
committed to disk. This is very fast when it works
but I wouldn't rely on it.

Please let me know if anyone has a better scheme for organizing scripts
or best practices for
passing "pdb"/"xyz" data to non-VMD programs that require pdb files for