VMD-L Mailing List

From: Zumot, Elia Nabil (enz1_at_pitt.edu)
Date: Fri Oct 14 2011 - 11:18:25 CDT

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