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

[Patrick Fuchs]

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