VMD-L Mailing List

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Mar 01 2012 - 00:13:58 CST

Albert,

It sounds like you need to work through our membrane tutorial for VMD/NAMD:

http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/mem-tutorial.pdf

Associated files needed to perform tutorial exercises:
https://netfiles.uiuc.edu/TCBG_Files/shared/membrane-tutorial-files.tar.gz

Also, you manually move independent molecules, representations, etc by
selecting from the menu: Mouse>Move> .... and then Atom, Residue, Fragment,
Molecule, or Rep. Then click on the molecule and drag to move, or
shift+click and drag to rotate. In your case, Molecule and/or Rep are
likely the best choices. How to further move molecules is covered more in
the main VMD tutorial and manual.

Main VMD tutorial:
http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html

VMD Manual:
http://www.ks.uiuc.edu/Research/vmd/current/ug/

Best,
Chris

On Wed, Feb 29, 2012 at 11:54 PM, Albert <mailmd2011_at_gmail.com> wrote:

> Hi Chris:
> I mean "not correct" means: after I superimposed my protein with OPM, I
> found that the membrane in the URL I mentioned in different directions
> comparing to the aligned protein, it is impossible just simple merge two
> PDB files to construct a membrane system....
>
> thanks
>
>
> On 03/01/2012 04:35 AM, Chris Harrison wrote:
>
> What do you mean the position is "not correct?" Please be more specific.
> The protein is too high/low in the membrane; the protein is at an
> incorrect angle to the membrane's normal axis; there's a big gap of lipids
> between protein and the membrane that floods with water; etc ....
>
>
>
> On Wed, Feb 29, 2012 at 3:33 PM, Albert <mailmd2011_at_gmail.com> wrote:
>
>> Hello:
>>
>> I've superimposed my homology models with related OPM protein. And now
>> I would like to embed my protein to pre-equilibrated membrane POPE from
>>
>> http://terpconnect.umd.edu/~jbklauda/research/download.html
>>
>> But I found that the position is not correct for the membrane.... Does
>> anybody have any idea how to do it? I am going to use CHARMM36 based POPE
>> for my aligned protein.
>>
>> THX
>>
>
>
>
> --
> Chris Harrison, Ph.D.
> NIH Center for Macromolecular Modeling and Bioinformatics
> Theoretical and Computational Biophysics Group
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>
>
>
>
> 

-- 
Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
http://www.ks.uiuc.edu/Research/namd       Voice: 773-570-6078
http://www.ks.uiuc.edu/~char                          Fax: 217-244-6078