[gmx-users] Creation of an index file with seperate lipid leaflets

[Alan Dodd]

Thanks to all for your help/suggestions.  I gave up on
modifying make_ndx, the code is just too impenetrable
for a weekend scripter like me...  Have made a perl
script to produce a .ndx file with 2 groups, one
containing all upper leaflet atoms, the other lower.

--- Patrick Fuchs <Patrick.Fuchs at ebgm.jussieu.fr>
wrote:

> Hi,
> I've written a python script that does what you
> want.
> I cleaned the script (make_2leaflets_index) and put
> it on my web page at 
> the following URL:
>
http://condor.ebgm.jussieu.fr/~fuchs/download/index.html
> Hope it helps.
> Ciao,
> 
> Patrick
> 
> Jay Mashl a écrit :
> > Wasted work would be bad ;)
> > 
> > Rather than headgroup orientation, maybe try
> looking at atom distributions 
> > along the bilayer normal direction.  Neutron
> scattering experiments show that 
> > for atom groups far from the bilayer midplane, the
> corresponding z-coordinates 
> > form two distinct distributions.  So one way could
> be the following. Pick a 
> > headgroup atom and obtain its z-coordinate. Have
> make_ndx accept this value as 
> > input. Search the system by looping over lipids
> and ask whether that atom type 
> > has a z-coordinate within some amount around the
> input value. From this you 
> > know the membership of the leaflets.  A more
> automatic way would be to have the 
> > program first discern the distribution and then
> reread the system to decide the 
> > leaflet membership.
> > 
> > Jay
> > 
> > 
> > On Wed, 8 Nov 2006, Alan Dodd wrote:
> >> Wouldn't shuffle/sort undo all the good work?  I
> did
> >> wonder if I should have labelled the lipids in
> >> different leaflets as different molecule types,
> or
> >> different chains, but it's a bit late now...
> >>
> >> --- Jay Mashl <mashl at uiuc.edu> wrote:
> >>
> >>> On Wed, 8 Nov 2006, Alan Dodd wrote:
> >>>> Has anyone already created a way to generate an
> >>> index
> >>>> file with the atoms from the two leaflets of a
> >>> bilayer
> >>>> listed seperately?  I can't believe it hasn't
> >>> already
> >>>> been done, but can't find a direct description
> of
> >>> a
> >>>> solution.  I'm attempting a modification to
> >>> make_ndx,
> >>>> (or perhaps something considerably less
> ambitious,
> >>>> judging by the way it's going so far) to permit
> >>> lipid
> >>>> selection based on headgroup orientation,
> though
> >>> I'd
> >>>> quite like to save myself the effort.
> >>>> Incidentally, splitres and splitat seem to be
> the
> >>>> wrong way around, unless I'm misunderstanding
> them
> >>> -
> >>>> they do the opposite of what they say.  From
> the
> >>>> gromacs 3.3.1 source download I did on April of
> >>> this
> >>>> year.
> >>> Reordering the lipids into leaflets in your
> starting
> >>> coordinate 
> >>> file might be a good idea. If you anticipate
> lipid
> >>> exchange between leaflets, 
> >>> then a more general tool like what you suggest
> would
> >>> be helpful.
> >>>
> >>> Jay
> >>>
> >>> _______________________________________________
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> >>
> >>
> >>
> >>  
> >>
>
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> 
> -- 
>
_______________________________________________________
> Patrick FUCHS
> Equipe de Bioinformatique Genomique et Moleculaire
> INSERM U726, Universite Paris 7
> Case Courrier 7113
> 2, place Jussieu, 75251 Paris Cedex 05, FRANCE
> Tel : +33 (0)1-44-27-77-16 - Fax : +33
> (0)1-43-26-38-30
> E-mail : Patrick.Fuchs at ebgm.jussieu.fr
> Web Site: http://www.ebgm.jussieu.fr/~fuchs
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