VMD-L Mailing List

From: Jon (teojy_at_bii.a-star.edu.sg)
Date: Mon Sep 24 2012 - 03:56:59 CDT

Dear all,
I have 2 questions that are linked somewhat.

First, I am trying to extract the time series of the chi1 angles of the
various residues from an AMBER trajectory. In addition, I would like to
define chi angles using the definition/atom selections here
(http://www.msg.ucsf.edu/local/programs/garlic/commands/dihedrals.html).
However, I am not aware of any function that does this easily using VMD,
unless I code everything in tcl from scratch. Is there an existing way
of doing this elegantly?

Second, my current solution is to use gromacs' g_chi function instead.
For this to work, I first converted AMBER's trajectory file (.mdrcd or
.netcdf) to gromacs file format. I tried this implementation
(http://easybioinfo.free.fr/?q=content/amber-trajectory-gromacs-xtc-conversion),
but it creates a single pdb file for every frame and is rather slow on
my computer. So instead, I tried a VMD approach by first loading the
trajectory with the relevant topology file into VMD, and then using the
'save coordinates' function from the GUI. This works beautifully, but I
would like to automate the process using tcl instead.

I could load the trajectory from tcl using the mol command. What I can't
seem to figure out is how to save the coordinates the same way. Is there
some way to accomplish this using tcl?

Any help will be greatly appreciated, thank you!

Jon