VMD-L Mailing List
From: Albert (mailmd2011_at_gmail.com)
Date: Wed Feb 29 2012 - 23:54:00 CST
- Next message: Chris Harrison: "Re: how to place a membrane protein with OPM ?"
- Previous message: Albert: "Re: how to place a membrane protein with OPM ?"
- In reply to: Chris Harrison: "Re: how to place a membrane protein with OPM ?"
- Next in thread: Chris Harrison: "Re: how to place a membrane protein with OPM ?"
- Reply: Chris Harrison: "Re: how to place a membrane protein with OPM ?"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
> <mailto: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
> <http://terpconnect.umd.edu/%7Ejbklauda/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 <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>
>
- Next message: Chris Harrison: "Re: how to place a membrane protein with OPM ?"
- Previous message: Albert: "Re: how to place a membrane protein with OPM ?"
- In reply to: Chris Harrison: "Re: how to place a membrane protein with OPM ?"
- Next in thread: Chris Harrison: "Re: how to place a membrane protein with OPM ?"
- Reply: Chris Harrison: "Re: how to place a membrane protein with OPM ?"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]