[gmx-users] Re: protein in popc

[Venky Krishna]

the command "genbox" will automatically take care of overlapping  
lipids and water molecules with the protein, and make a hole and also  
insert the protein into the bilayer.. there is no prior requirement  
of making a hole in the popc bilayer.

Here is quite an in-detail protocol for protein insertion into a  
bilayer.
http://www.dddc.ac.cn/embo04/practicals/9_16.htm

Venky

Venky Krishnamani
Dr.Janos K. Lanyi Lab,
D320, Medical Sciences D
University of California, Irvine


On May 15, 2006, at 5:13 AM, Shulin Zhuang wrote:

> I am very new to membrane modeling and hope to see more up-to-date  
> protocols. Wish anyone can share it with us.
>
> On 5/15/06, Graham Smith <graham.smith at biiuk.com> wrote:
>
> > Message: 2
> > Date: Mon, 15 May 2006 02:32:06 -0700 (PDT)
> > From: mahbubeh zarrabi < zarrab_m at yahoo.com>
> > Subject: [gmx-users] protein in popc
> > To: gmx-users at gromacs.org
> > Message-ID: < 20060515093206.21682.qmail at web51605.mail.yahoo.com>
> > Content-Type: text/plain; charset=iso-8859-1
> >
> > dear freinds
> > I have made a hole in POPC128a bilayer.But I failed
> > inputing protein into it.I run below commands but
> > there is not protein in the hole.whould you please
> > help me? do you have another
> >  protocol for protein insertion in popc (in detail)?
> >
> > make_hole.pl -f popc.pdb -o popcout.pdb -r 1.4 -lipat
> > P8 -lipid POP -cx 2.3 -cy 2.8
> > grompp -f run.mdp -o insert.tpr -c popcout.pdb -p
> > popc.top
> > mdrun -v -hole -holep hp.mdp -deffnm insert
> > -----------------------------------------------------
>
> Dear Mahbubeh,
>
> I don't know if more up-to-date protocols have since been developed, I
> don't work on membrane proteins any more. However, if you still  
> want to
> try to use the older hole-making code:
> Checks:
> (a) you are using a special version of mdrun compiled from old gromacs
> version 3.1.4 and the extra code available from the contributions  
> section
> (b) you have looked at the html-format tutorial notes.
> (c) "Hole-making" forces are being generated and applied to certain
> atoms: to see this, run with
> debugsurf                = yes
> in the hp.mdp files and it will stop at step 0 after producing extra
> pdbs with the dummy atoms to show the forces (see tutorial)
> (d), Finally, the output of mdrun -v -hole -holep hp.mdp... will not
> have the protein inserted directly, but will just have a hole in the
> right place for your protein to be put in (by combining the pdb or gro
> files with an editor).
>
> Graham
> --
> Dr Graham R. Smith
> Head of Protein-Protein Interactions
> Biosystems Informatics Institute
> Newcastle upon Tyne
> NE1 4EP
>
>
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>
> -- 
>    Shulin Zhuang
> Chemistry Department
> Zhejiang University PRC
> shulin.zhuang at gmail.com
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