VMD-L Mailing List

From: Florian Haberl (Florian.Haberl_at_chemie.uni-erlangen.de)
Date: Tue Nov 16 2004 - 03:32:41 CST

Hi all,

>   I want it for furhter md simulations. I tried the membrane package
> http://www.ks.uiuc.edu/Research/vmd/plugins/membrane/
> but i somehow can not put the protein in the membrane. Every time i try
> that it gets out from the other side.

i would suggest you switch to gromacs (to be found on www.gromacs.org )
under contributions you can found what you are searching for (i think):

[quote]
mdrun modified to make a hole in a lipid bilayer
 A modified version of mdrun that can be used to make a hole in a lipid
bilayer that is the right shape to drop in the membrane protein of your
choice. It does this by reading a molecular surface file made by Grasp or
MSMS. It can also make a cylindrical hole. Tar file contains documentation
...
[/quote]

read mailing list and readme for further information

Greetings,

Florian

> thanks for writing back.
> Nitin
>
> On Mon, 15 Nov 2004, Florian Haberl wrote:
> > Hi all,
> >
> > On Monday 15 November 2004 02:20, Nitin Bhardwaj wrote:
> > > Hi,
> > >   I want to surround my protein with a lipid bilayer completely (in
> > > case of trans-membrane protein) or partially (in case of
> > > membrane-binding ones).
> > > I can generate a lipid bilayer in VMD using the package and command
> > > 'membrane' but I do not know how to put this lipid layer at a
> > > particular orientation to the protein.
> > > I would appreciate any help.
> > > thanks,
> > > Nitin
> >
> > Do you want this only for visual aspects or do you want further md
> > simulations?
> >
Greetings,

Florian 

-- 
-------------------------------------------------------------------------------
 Florian Haberl                            Universitaet Erlangen/
 Computer-Chemie-Centrum    Nuernberg
                                                      Naegelsbachstr. 25
                                                      D-91052 Erlangen
  Mailto: florian.haberl AT chemie.uni-erlangen.de
 -------------------------------------------------------------------------------

attached mail follows:

Hi all,

> I want it for furhter md simulations. I tried the membrane package
> http://www.ks.uiuc.edu/Research/vmd/plugins/membrane/
> but i somehow can not put the protein in the membrane. Every time i try
> that it gets out from the other side.

i would suggest you switch to gromacs (to be found on www.gromacs.org )
under contributions you can found what you are searching for (i think):

[quote]
mdrun modified to make a hole in a lipid bilayer
 A modified version of mdrun that can be used to make a hole in a lipid
bilayer that is the right shape to drop in the membrane protein of your
choice. It does this by reading a molecular surface file made by Grasp or
MSMS. It can also make a cylindrical hole. Tar file contains documentation
...
[/quote]

read mailing list and readme for further information

Greetings,

Florian

> thanks for writing back.
> Nitin
>
> On Mon, 15 Nov 2004, Florian Haberl wrote:
> > Hi all,
> >
> > On Monday 15 November 2004 02:20, Nitin Bhardwaj wrote:
> > > Hi,
> > > I want to surround my protein with a lipid bilayer completely (in
> > > case of trans-membrane protein) or partially (in case of
> > > membrane-binding ones).
> > > I can generate a lipid bilayer in VMD using the package and command
> > > 'membrane' but I do not know how to put this lipid layer at a
> > > particular orientation to the protein.
> > > I would appreciate any help.
> > > thanks,
> > > Nitin
> >
> > Do you want this only for visual aspects or do you want further md
> > simulations?
> >
Greetings,

Florian 

-- 
-------------------------------------------------------------------------------
 Florian Haberl                            Universitaet Erlangen/
 Computer-Chemie-Centrum    Nuernberg
                                                      Naegelsbachstr. 25
                                                      D-91052 Erlangen
  Mailto: florian.haberl AT chemie.uni-erlangen.de
 -------------------------------------------------------------------------------