VMD-L Mailing List

From: xiaoqin huang (xqhuang1018_at_msn.com)
Date: Wed Apr 05 2006 - 17:05:39 CDT

Yes, that is good, I switch to 32-bit version of vmd-1.8.3, and now it can
safely load membrane.
the next question is to align the protein with membrane, is ther any good
way to align them exactly by superimposing along X,Y,Z axes?
in a tutorial saying "Hold down the shift-key to rotate them separately...".
this is difficult to get a good alignment for the protein with the membrane.

appreciate any good help!

xiaoqin

04/05/2006

>From: John Stone <johns_at_ks.uiuc.edu>
>To: xiaoqin huang <xqhuang1018_at_msn.com>
>CC: vmd-l_at_ks.uiuc.edu
>Subject: Re: vmd-l: membrane loading
>Date: Wed, 5 Apr 2006 14:32:38 -0500
>
>
>Hi,
> I believe this is caused by a dynamic loading problem with psfgen on
>IRIX.
>Can you try running the 32-bit version of VMD on your SGI and see if you
>still
>encounter the problem? This is a particularly odd problem that has cropped
>up
>as a result of a particular version of the SGI compilers used to build VMD.
>Let me know if you still have this problem with the 32-bit version of VMD.
>
> John
>
>On Wed, Apr 05, 2006 at 03:25:12PM -0400, xiaoqin huang wrote:
> > Can anyone help me to see what is the problem when loading membrane?
> > I did it in ths way on Fuel workstation of SGI with IRIX64 system
> >
>-----------------------------------------------------------------------------------------
> > #in the shell
> > vmd
> > # in vmd console
> > package require membrane
> > #comes out
> > 1.0
> > #command
> > membrane -l POPC -x 60 -y 60
> > #result in:
> > the whole vmd process is killed, and all the windows disappeared,
>produce a
> > core
> >
>-----------------------------------------------------------------------------------------------------------------
> >
> > I installed vmd-1.8.4b11, and the membrane plugin should be ok as the
> > membrane command works.
> >
> > thanks.
> >
> > xiaoqin
> >
> > 04/05/2006
> >
>
>--
>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