From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Oct 14 2011 - 15:09:44 CDT

Easiest solution: http://www.ks.uiuc.edu/~gumbart/files/POPE-C36/

On Oct 14, 2011, at 11:18 AM, 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
>