VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 10 2006 - 11:35:44 CDT
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- In reply to: xiaoqin huang: "water layers"
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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
- Next message: Noriaki Okimoto: "multiple peptides simulation"
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- In reply to: xiaoqin huang: "water layers"
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