From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 26 2009 - 10:04:16 CDT

Joshua,
  Hmm, it looks like the Mac builds had a problem on Friday that I
didn't notice previously. I'll do a fresh set of builds and let you
know when I have them ready for you.

Cheers,
  JOhn

On Sat, Oct 24, 2009 at 11:42:12PM -0400, Joshua Adelman wrote:
> Hi John,
>
> I downloaded the newest os x x86 binary of VMD from biocore (link/
> filename says the .dmg contains 1.8.8a4, but the actual binary reports
> 1.8.8a3). I'm still running into problems when I try to use mdff sim,
> where I get the error asking me to identify the location of VMD, I
> give it the app location and it says its not executable and then fails
> to find volutil.
>
> I just wanted to let you know that this error is still there in the
> newest build (at least the OSX for x86).
>
> Josh
>
>
> On Oct 19, 2009, at 4:27 PM, John Stone wrote:
>
> >
> >Joshua,
> > I should have a new test build posted on biocore late this week.
> >I've been working hard on adding basic OpenCL infrastructure and the
> >first couple of OpenCL kernels into VMD and as a result I've been
> >spending a fair amount of my time working around various small bugs
> >in the beta OpenCL implementations I'm working with presently.
> >I'll should have fresh test builds posted on Thursday if all goes
> >well.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Sun, Oct 18, 2009 at 11:19:28PM -0400, Joshua Adelman wrote:
> >>Hi Leo,
> >>
> >>Thanks for your response. Any idea of when the new build might be
> >>posted on biocore? I can probably get access to a linux machine, but
> >>it would definitely be easier to have a working os x version.
> >>
> >>Josh
> >>
> >>On Oct 17, 2009, at 4:26 PM, Leonardo Trabuco wrote:
> >>
> >>>Dear Joshua,
> >>>
> >>>On Fri, Oct 16, 2009 at 4:20 PM, Joshua Adelman <jla65_at_pitt.edu>
> >>>wrote:
> >>>>I am attempting to use the MDFF plugin that is available in the
> >>>>development
> >>>>version of VMD. I downloaded VMD 1.8.8a1 for Intel-based OSX
> >>>>machines from
> >>>>Biocore. As a side note, the disk image is named properly, but for
> >>>>some
> >>>>reason the name of the vmd app is named 1.8.7 (when running VMD it
> >>>>displays
> >>>>the correct version number though).
> >>>
> >>>Right, John Stone is aware that he needs to change the disk image
> >>>for
> >>>the next Mac builds. :-)
> >>>
> >>>>After issuing the "require package mdff" commend (returns version
> >>>>0.2), I
> >>>>attempt to build a simulated map using "mdff sim". When I issue the
> >>>>tcl
> >>>>command, I get a pop-up window:
> >>>>"Could not locate '/Applications/VMD'"
> >>>>
> >>>>And then it asks if I'd like to identify the path. When I select
> >>>>the VMD
> >>>>app, I get a warning that '/Application/VMD 1.8.8a1.app' is not
> >>>>executable.
> >>>>
> >>>>The mdff sim routine still runs, but it fails when it tries to make
> >>>>use of
> >>>>volutil (I assume this is what it needs to identify the VMD app in
> >>>>order to
> >>>>find it). I don't get any further error messages, but basically it
> >>>>never
> >>>>completes the low-pass filtering step, because it doesn't know
> >>>>where volutil
> >>>>lives.
> >>>
> >>>We are also aware of this problem, but haven't got around
> >>>preparing a
> >>>new build addressing it yet. According to John, we need to fix the
> >>>plugin builds so they use the path-relative Tcl library if they are
> >>>compiled against the VMD Tcl library rather than the system-provided
> >>>one.
> >>>
> >>>>Any suggestions would be most appreciated.
> >>>
> >>>Please wait until a new Mac build is posted on biocore. Or, if you
> >>>can, give the Linux version a try for now.
> >>>
> >>>Thanks,
> >>>Leo
> >>>
> >>>>Josh
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>>--
> >>>Leonardo Trabuco, Ph.D. candidate
> >>>Theoretical and Computational Biophysics Group
> >>>University of Illinois at Urbana-Champaign
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
> --
> Dr. Joshua L. Adelman
> Postdoctoral Researcher - Grabe Lab
> Department of Biological Sciences
> University of Pittsburgh, Pittsburgh, PA
> email: jla65_at_pitt.edu
> mobile: 510.220.0396
>
>

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078