VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 20 2020 - 15:31:19 CDT

Viktor,
  Thanks, I grabbed your test files, and I've got the version of Josh's
patch that he had subsequently corrected to properly deal with your
fourth example file.

I will proceed by testing the updated version of Josh's patch on Windows,
against your files and any that I'm able to get from other volunteers, if
things look good there and on Unix, then I might be able to get this
into an upcoming round of test builds. That being said, please feel
free to compile Josh's patched source file on your own system and do
testing yourself as well.

Best,
  John

On Tue, Oct 20, 2020 at 10:38:06PM +0300, viktor wrote:
> ?? Tue, 20 Oct 2020 14:28:12 -0500
> John Stone <johns_at_ks.uiuc.edu> ??????????:
>
> > Hi Viktor, Josh,
> > This has been on my TODO list, but it has been behind other higher priority
> > items since it doesn't affect as many users as some other problems ddid,
> > and since plugins can easily be compiled outside of VMD by users and
> > loaded on-demand at runtime.
> >
> > Viktor: Did you try using the patched plugin source
> > code that Josh posted back in February? I hadn't heard any followup
> > from anyone since that discussion.
> >
> > One thing I need that would make it a lot easier for me to accept
> > Josh's patch would be several example AMBER restart file test cases.
> >
> > The patch Josh sent changes multiple aspects of how the parsing works
> > so that it will also skip over optional velocity data, so these are
> > things that need to be tested carefully, not only on Unix where I'm
> > sure he has done sufficient testing himself, but also on Microsoft Windows,
> > where some of the file I/O APIs have different behavior than they do
> > on Unix.
> >
> > I'm perfectly happy to do that testing, but I need example
> > AMBER files to test with. If you can provide some, that would
> > be very helpful to me and would make it possible for me to work through
> > this much sooner, particularly now that I have up-to-date Windows
> > builds of VMD for both 32-bit and 64-bit Windows working locally.
> >
> > Best,
> > John Stone
> >
> > On Tue, Oct 20, 2020 at 12:02:03AM +0300, viktor wrote:
> > > Seems like patch hasn't been included in any of the alpha releases since February. Any troubles
> > > with it?
> > >
> > > --
> > > 73, Viktor
> >
>
> I can do more thorough testing soon. You can use my original example tarball located here
> (https://ftp.desolve.ru/ftp/viktor/vmd_test.tar.gz)
>
> --
> 73, Viktor 

-- 
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/