VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Sat Oct 24 2009 - 22:42:12 CDT

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