VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Oct 14 2011 - 13:38:52 CDT

On Fri, Oct 14, 2011 at 12:37 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> They are in the VMD plugins CVS tree.

or bundled with recent VMD alpha test binaries.

axel.

>
> Cheers,
>  John Stone
>  vmd_at_ks.uiuc.edu
>
> On Fri, Oct 14, 2011 at 12:18:25PM -0400, Zumot, Elia Nabil wrote:
>> Hi JC,
>>
>> Could you please place the files (CHARMM36 membrane builder) somewhere we can all copy/download them?
>>
>> Thank you
>>
>>
>>
>> Elia Zomot, PhD
>> Computational and Systems Biology Department
>> School of Medicine, University of Pittsburgh
>> 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
>> Voice: 412 648 7785 - Fax: 412 648 3163
>> enz1_at_pitt.edu
>> ________________________________________
>> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] On Behalf Of JC Gumbart [gumbart_at_ks.uiuc.edu]
>> Sent: Wednesday, September 21, 2011 12:44 PM
>> To: 'John Stone'; 'Maggie Pruitt'
>> Cc: vmd-l_at_ks.uiuc.edu
>> Subject: RE: vmd-l: Problem building POPE membrane with plugin using CHARMM36
>>
>> It's because I forgot to include the necessary files for POPE in the CVS
>> when VMD 1.9 was built (I put them in on 5/8 though).  I'll send you the
>> files off-list shortly.
>>
>>
>> -----Original Message-----
>> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
>> John Stone
>> Sent: Wednesday, September 21, 2011 11:33 AM
>> To: Maggie Pruitt
>> Cc: vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: Problem building POPE membrane with plugin using
>> CHARMM36
>>
>> Hi,
>>   This looks to me like it might be a bug in the membrane builder plugin
>> where it is not correctly handling filenames that contain spaces.
>> I will have a look at it today.
>>
>> Cheers,
>>   John Stone
>>   vmd_at_ks.uiuc.edu
>>
>> On Mon, Sep 19, 2011 at 12:19:41PM -0500, Maggie Pruitt wrote:
>> > Dear VMD Community,
>> >
>> > I'm trying to build a protein-membrane system following the Membrane
>> Proteins Tutorial.  However, I keep receiving the error pasted below each
>> time I try to build a POPE membrane with the Membrane Builder plugin using
>> the CHARMM36 topology file (VMD 1.9 MacOS X OpenGL, CUDA (Intel x86)).
>> Could anyone please give me some insight into what is wrong?  Or could this
>> be a bug in VMD 1.9?  If it helps, I can successfully build a POPC membrane
>> with the plugin using C36 and also a POPE membrane using C27.
>> >
>> > Thanks in advance for your help,
>> >
>> >
>> > Maggie Pruitt
>> >
>> >
>> > ERROR: Unable to open psf file /Applications/VMD
>> 1.9.app/Contents/vmd/plugins/noarch/tcl/membrane1.1/pope36_box.psf
>> > MOLECULE DESTROYED BY FATAL ERROR!  Use resetpsf to start over.
>> > ERROR: Unable to open psf file /Applications/VMD
>> 1.9.app/Contents/vmd/plugins/noarch/tcl/membrane1.1/pope36_box.psf
>> > MOLECULE DESTROYED BY FATAL ERROR!  Use resetpsf to start over.
>> >     while executing
>> > "readpsf $psffile"
>> >     (procedure "membrane_core" line 81)
>> >     invoked from within
>> > "membrane_core -l "$uselipid" -x "$xdim" -y "$ydim" -o "$prefix" -top
>> "$useTop""
>> >     (in namespace inscope "::Membrane" script line 4)
>> >     invoked from within
>> > "::namespace inscope ::Membrane {
>> >         puts "membrane_core -l $uselipid -x $xdim -y $ydim -o $prefix -top
>> $useTop"
>> > #        membrane_core -l POPC -x..."
>> >     invoked from within
>> > ".membrane.gobutton invoke"
>> >     ("uplevel" body line 1)
>> >     invoked from within
>> > "uplevel #0 [list $w invoke]"
>> >     (procedure "tk::ButtonUp" line 23)
>> >     invoked from within
>> > "tk::ButtonUp .membrane.gobutton"
>> >     (command bound to event)
>>
>> --
>> NIH Resource 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/       Fax: 217-244-6078
>>
>
> --
> NIH Resource 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/       Fax: 217-244-6078
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.