VMD-L Mailing List

From: Rose, Stuart Wallace (swrose_at_illinois.edu)
Date: Wed Dec 30 2015 - 09:55:01 CST

Hello,

In the MDFF tutorial under "A simple MDFF example" the step requiring this command does not work using VMD for WIN32, version 1.9.2 (December 29, 2014):

mdff sim $sel -res 5 -o 4ake-target autopsf.situs

No situs file is generated and no alternative file extension/ types are referenced in documentation or posts in the context of the "sim" command or the "-o" option. By the way neither is there any working code available to anyone outside of the Schulten group.

Earlier post mentions things like the inability to generate a situs formatted file and the situs web page for vmd mention vmd can read but not write this format. MDFF documentation is sparse regarding command examples, reasons for option and what anything does. Is there a special place to find out how this stuff works because the first steps of the tutorial fail so there is a high probability of a long path of problems.

Brief description of file formats and context for MDFF are necessary for outsiders to gain actual knowledge of the tools use.

Regards,
Stuart

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Stuart W. Rose E-Mail: swrose_at_illinois.edu
University of Illinois @ Urbana-Champaign Office: 153 Davenport Hall
607 S. Mathews Avenue
Urbana, IL 61801
                                                                               Lab Ph. (217)333-7407
Center for Biophysics & Quantative Biology Office: Loomis, MC-704
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