VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Wed Dec 30 2015 - 12:35:30 CST

I missed it the first time reading your email, but it looks like the
problem is the file name you are writing. In your first email you said the
following command produced no output:

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

You seem to have a space between 'target' and 'autopsf.situs'. As shown in
the tutorial, there should be an '_' between them, so it is one file name.

On Wed, Dec 30, 2015 at 12:11 PM Rose, Stuart Wallace <swrose_at_illinois.edu>
wrote:

> Hello,
>
> Thank you for your help but your first paragraph is wrong for me. In the
> command window a file write is performed into a temp folder with an mdff
> prefix and .dx suffix. There is no file written in any of the
> aforementioned directories, including the working directory that I had set,
> with the situs suffix or the file prefix designated by the mdff command.
>
> My question would be how to I make this command work on a windows system
> because "mol new... " finds nothing either:
> mdff sim $sel -res 5 -o 4ake-target autopsf.situs
>
>
> I cannot find any working examples of scripts using mdff or usage
> information for the "-o" option. Simply stating its existence is
> insufficient for a programmer to begin using it without context. I would
> like to know what types of files the "-o" option is capable of outputting
> and how it needs the file (file name) it is outputting to. That is, is the
> argument for the -o option a full file path or string of Linux file or
> Windows file format. I am sorry that my time is limited and I do not have
> time for trial and error programming from the very first example.
>
> Thank you for noting that the extensive use of the mdff software and the
> outreach program funded should produce a substantial body of useful script
> help and actual working examples. Could you please tell me where to look?
>
>
>
> *********************************************************************************
> 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
>
> *********************************************************************************
> ------------------------------
> *From:* Ryan McGreevy [ryanmcgreevy_at_ks.uiuc.edu]
> *Sent:* Wednesday, December 30, 2015 10:51 AM
> *To:* Rose, Stuart Wallace; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: mdff: tutorial
>
> If you are running VMD on windows, the issue you are having is likely due
> to how Windows treats 32bit applications running on 64bit windows. If you
> 'ls' from the tkconsole, you should notice that the output file appears to
> be there. You can load it or run commands on it from the tkconsole/VMD as
> normal (i.e. mol new 4ake-target_autopsf.situs should work). However, if
> you try to navigate to that file in windows explorer, it won't appear to
> be there. The actual output file should be written to the
> folder C:\Users\UserName\AppData\Local\VirtualStore\Program Files
> (x86)\University of Illinois\VMD where UserName is your windows user
> name, and assuming you performed a default install. This is the folder that
> windows tricks VMD into thinking is the normal C:/ path.
>
> I am not sure what you mean by "By the way neither is there any working
> code available to anyone outside of the Schulten group." All MDFF code has
> been publicly available in VMD and NAMD for many years now with many people
> external to our group successfully using it. Along with the tutorial, you
> can find more information about the MDFF plugin at
> http://www.ks.uiuc.edu/Research/vmd/plugins/mdff/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_plugins_mdff_&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=z2ogsss5o7-95rDwkRe8zf2bKCnyTShHK6Vexa1An18&m=gKoyya8OWkifX9tvIjZ9zxqJsxpklyn9MSY0mIbNSAc&s=Q_hPO6xg1JtpSPGiYXZWpiZJeKRfytZalHmzY0dqTNQ&e=> or
> by typing each command in the vmd console without any options to get its
> usage. The sim command can generate .situs and .dx files, but you are
> correct that the documentation lacks this information, which I will make
> sure is correctly updated. Also, for more detailed information on the
> theoretical and practical aspects of MDFF, you can read the MDFF
> methodological publications:
> http://www.ks.uiuc.edu/Research/mdff/publications.html
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_mdff_publications.html&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=z2ogsss5o7-95rDwkRe8zf2bKCnyTShHK6Vexa1An18&m=gKoyya8OWkifX9tvIjZ9zxqJsxpklyn9MSY0mIbNSAc&s=WyfkHpMLVEdqc4yAj0v59Y9RQsHB3nvH2o5qF-Gp_d0&e=>
>
> On Wed, Dec 30, 2015 at 10:31 AM Rose, Stuart Wallace <swrose_at_illinois.edu>
> wrote:
>
>> 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
>>
>>
>> *********************************************************************************
>> 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
>>
>> *********************************************************************************
>>
>