VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Nov 01 2020 - 01:36:58 CDT
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Hi,
I worked through fixing some minor remaining issues with the
patched rst7plugin Josh sent and I've integrated it and re-tested
it with the four combinations of AMBER 18 restart cases that were
provided previously. I spent some extra time doing a little
housecleaning on the code so that it's better commented and
easier to understand since it has gotten a little more complex now.
The code is committed and the next test builds will have
the new plugin included in them by default.
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/
- Next message: John Stone: "Re: Molefacture 2.0 - missing functionality?"
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- In reply to: viktor: "Re: VMD doesn't handle AMBER Restart files correct"
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