New version of Molefacture -small molecule modeling tool- posted

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Wed Jul 10 2019 - 16:59:50 CDT

Dear all,

The new VMD alpha version posted today also releases the new version of Molefacture (small molecule modeling tool). The latest version is substantially different, with improved usability, new building functions, and structure clean-up/minimize.

Also new is the interface with the CGenFF program/web server. Although both teams are still developing the authentication process from a direct connection between VMD and CGenFF web server, the Molefacture user can already export the molecule to a mol2 file, and add the stream file returned by the server to Molefacture.

It is also possible to export unparameterized molecules from QwikMD to Molefacture to add hydrogen atoms, fetch topologies and parameters in the form of a stream file, and then send back to QwikMD to continuing preparing the simulation. The export process is done from the "Edit Atoms" window in QwikMD.

For more information, please check the Molefacture webpage http://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/, and let us know your feedback, issues and suggestions.

Best,

João Ribeiro
Research Programmer
 
Beckman Institute for Advanced Science and Technology
NIH Center for Macromolecular Modeling & Bioinformatics
University of Illinois at Urbana-Champaign
405 N. Mathews Avenue | M/C 251
Urbana, IL 61801
217.300.5851 | jribeiro_at_illinois.edu
www.ks.uiuc.edu/

On 7/10/19, 3:29 PM, "John Stone" <owner-vmd-l_at_ks.uiuc.edu on behalf of johns_at_ks.uiuc.edu> wrote:

    Hi,
      I've just posted two new Linux and MacOS X test binaries
    of VMD 1.9.4 alpha 35. The new version includes new structure
    building plugins, a new colvars dashboard tool, updates to the
    RTX-accelerated ray tracing engines to quash one of the
    outstanding bugs that people had run into with previous builds.
    
    I expect that we will begin a more rapid update cycle soon because
    we have also made some massive updates to VMD's Python support with
    contributions from Robin Betz and others, and I'm looking for a
    good way to redistribute pre-built VMD binaries that are linked
    against the latest Python 3.x versions.
    
    We will have alpha builds for other platforms (various Windows and
    64-bit MacOS X) starting to become available as bugs get reported
    and quashed in the new plugins.
    
    Some of the contributors to the new tools in this beta will
    followup on this email with specifics of the new features/tools
    they've added for those eager to try them out.
    
    Best regards,
      John Stone
      vmd_at_ks.uiuc.edu
    
    
    --
    NIH Center for Macromolecular Modeling and Bioinformatics
    Beckman Institute for Advanced Science and Technology
    University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
    http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
    http://www.ks.uiuc.edu/Research/vmd/
    
    

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