From: John Stone (
Date: Thu Nov 30 2000 - 14:51:44 CST

Dear VMD-L,
  We have begun to collect together many of the smaller scale
programs and scripts written in our research group that others
in the field would find useful. We are calling this collection
"MDTools", and have created a web page (if you haven't already
seen it) for these tools:

Here's a brief list of the MDTools we've recently made available:

      Chemical2vmd Lets VMD act as a helper application for
                      chemical/x-vmd MIME type

        Conect2psf Converts PDB CONECT records into a PSF file for
                      proper bond display in VMD

    FlipDCD/FixDCD DCD file endianism and header conversion
MDTools for Python Protein structure and dynamics analysis classes

            MatDCD Matlab package for DCD reading/writing

             Mindy A "minimal" molecular dynamics program

            PDBCat Helpful tool for PDB text processing

            SODIUM Arrange ions around biological macromolecules

              Trio MD Trajectory file converter

          Usagemon Software usage/event tracking system

We hope that the community will find these tools useful in addition
to our larger development projects BioCoRE, NAMD, and VMD.

If you have any comments, questions, or suggestions for the MDTools page
please send email to me and I'll address them.

  John Stone

NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email:                 Phone: 217-244-3349              
  WWW:      Fax: 217-244-6078