From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Tue Jan 05 2016 - 00:47:27 CST

I managed to reproduce the problem by first changing the current directory
in the TkConsole before running the mdff sim command. I know what is
breaking but not why, so I don't have a proper fix yet. However, in the
meantime, you can work around the problem by launching VMD and not changing
the directory (i.e. load your molecule through the GUI or on the command
line specified by the full path. Similarly for command line output, write
the full path, or else just the file name alone which will write the output
file to the VirtualStore path I mentioned previously).

On Mon, Jan 4, 2016 at 11:39 PM JC Gumbart <gumbart_at_physics.gatech.edu>
wrote:

> Again, for me it works exactly as described. Clean install of VMD on
> Windows 8. All I could guess is some weird write permission issue? I get
> everything exactly the same as you up to this line:
>
> Info) volmap: writing file
> "C:/Users/arclab/AppData/Local/Temp/mdff_sim860592547
> 7392006.dx”.
>
> But then after I get “MAP <- “C:/Users/JC/AppData…”
>
> Regardless of the cause I do not expect more or updated documentation
> would help in this case, which seems to be an issue specific to your
> computer. There are often little Windows issues that are missed in most
> tests because it does things differently than Unix / Macs.
>
> Best,
> JC
>
> On Jan 4, 2016, at 10:07 PM, Rose, Stuart Wallace <swrose_at_illinois.edu>
> wrote:
>
> One more time:
>
> I have a production system.
>
> Running version 1.9.2
>
> I ran the same MDFF tutorial steps with autopsf.
>
> I received the following message:
> ERROR) could not read file 4ake-target_autopsf.situs
>
> The directory contained that file and the command window had a few
> messages like:
>
> situsplugin) Error reading voxel scale.
>
> I see that there was a previous entry into the mailing list regarding this
> exact issue. This is not a non issue. Others have had this problem.
> Your situs plugin page is not updated. There is no support / documentation
> that indicates any of this may, might or will work.
>
> Really?
>
>
>
>
> *********************************************************************************
> 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:* JC Gumbart [gumbart_at_physics.gatech.edu]
> *Sent:* Monday, January 04, 2016 1:28 PM
> *To:* Rose, Stuart Wallace
> *Cc:* Ryan McGreevy; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: mdff: tutorial
>
> Stuart - it works fine for me in Windows, and the file is exactly where
> Ryan says it is. Could you post the commands you ran before as well?
> Maybe there’s a problem with the selection?
>
> Best,
> JC
>
> On Dec 30, 2015, at 2:18 PM, Rose, Stuart Wallace <swrose_at_illinois.edu>
> wrote:
>
> Sorry for "miss copying" the line. The line I used and continue to try in
> my tk window in accordance with the tutorial instruction is:
> mdff sim $sel -res 5 -o 4ake-target_autopsf.situs
>
> The "_" (underline character) was left out of my post but I did not leave
> it out of the command when using it.
>
>
> *********************************************************************************
> 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 12:35 PM
> *To:* Rose, Stuart Wallace; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: mdff: tutorial
>
> 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--001a114a83e6f2a2920528909c9b--