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

Marc F. Lensink lensink at scmbb.ulb.ac.be
Wed Nov 8 17:50:50 CET 2006

On Wed, Nov 08, 2006 at 10:09:28AM -0600, Jay Mashl 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.

look at the z-coordinates of the phosphorus atoms and expand these
into full residues.  you probably don't have flip-flop, so this is a
static group.

you can do this using the gromacs libraries, but with some clever use
of logical operations you can also write a script around make_ndx.

if you're lazy, you can probably also do it using my program g_under
(contact off-list, i still haven't made a distribution).  nothing
against choosing a single water molecule as 'Peptide' and a cylinder
with dimensions 8x8x1 nm (assuming bilayer normal is in z-direction).
here's the help of the program:

g_under can do a number of things on a group of atoms that are located in a
specific direction under an other group.

Typically one will want to extract the lipid molecules that are directly
under a peptide that is binding to a membrane.

Two index groups are required; one describing the Peptide, and one describing
the Membrane. Subsequently all Membrane atoms that have all of their
coordinates (x, y and z) within a threshold value of any of the Peptide
atoms' x, y or z coordinate, are defined as being *under* the Protein.  The
threshold value in each direction is supplied with -d.

For every frame output is written to these files:
   -oa: all atom numbers of this group, starting at zero.
   -or: all unique residue numbers of this group, starting at one.

Output after this is affected by the operators set with -res and -and.

   -res expands the found atoms to include full residues
   -and gives the possibility to cross the resulting group with an other
index group using the AND operator.

When -od is given, the distance between the centers of mass of the resulting
group and an other group is calculated. The total distance and its x, y and z
components are plotted. This other group can have its atoms that make part of
the UNDER group excluded when -not is given. If -coord is supplied, also the
individual centre-of-mass coordinates of the two groups are plotted.


Marc F. Lensink           http://www.biochem.oulu.fi/~lensink/
Centre for Structural Biology and Bioinformatics         SCMBB
Université Libre de Bruxelles          lensink at scmbb.ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425

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