VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Tue Jan 12 2010 - 17:00:00 CST

Dear Joshua,

John just posted new VMD development builds on biocore that address a
Tcl linking problem that was preventing MDFF from working on the Mac.
This build also includes a fix for the error you saw when VMD failed
to find the volutil binary (there was an issue with a path containing
white spaces).

Please give this new build a try when you get a chance and let us know
if you have any problems. You might also want to check the updated
MDFF tutorial at: http://www.ks.uiuc.edu/Research/mdff/

Thanks,
Leo

On Sat, Oct 24, 2009 at 9:42 PM, Joshua Adelman <jla65_at_pitt.edu> 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
>
>
>
> 

-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign