VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 10 2006 - 11:35:44 CDT

Hi,
  You could use the 'solvate' plugin in VMD to add waters, or one of the
other solvent generation tools out there like SOLVATE (Grubmuller's),
Dowser, etc.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 07, 2006 at 03:08:38PM -0400, xiaoqin huang wrote:
> hi, all,
> anyone knows how to increase the thickness of water layers at both side of
> lipids? after the membrane complex is generated, more waters are needed to
> cover all the protein atoms.
> thanks!
>
> xiaoqin
>
> 04/07/2006
>
>
> >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 17:36:06 -0500
> >
> >Hi,
> > You can use the various atom selection commands such as
> >$sel move, $sel moveby, $sel lmoveby, etc... They are described
> >in the User's Guide here:
> > http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.3/ug/node107.html
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Wed, Apr 05, 2006 at 06:05:39PM -0400, xiaoqin huang wrote:
> >> 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
> >>
> >
> >--
> >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
> 

-- 
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