[gmx-users] RE: Insertion of protein in lipid bilayer

Graham Smith graham.smith at biiuk.com
Mon Aug 8 14:15:12 CEST 2005


Please look at the tutorial again - the paragraphs just after the
parameter table are the relevant ones.

Insidesurf.pdb gives an indication of atoms that have the extra force on
them. In order to indicate direction, each atom in the "real" system
that experiences the extra force, whatever its chemical type, is
duplicated into two virtual atoms; I make them carbon and nitrogen for
convenience but the chemical type doesn't mean anything. The C atom has
atom type CSF, (vmd "name" in the selection menu), and the N is NSF.
They are reside type FDUM (vmd selection "resname"). The C-N direction
shows the direction of the force.

The upshot of this is that insidesurf.pdb should show the lipids (and
water) that are inside your MSMS surface, but each will be doubled (as
if you had "double vision"), one in cyan and one dark blue (default vmd
colours I think).

If you don't see anything then the surface must be wrong.
molsurfpdb.pdb shows you where the program thinks the molecular surface
is - again you should see a double shell, cyan and dark blue. Again
carbon and nitrogen virtual atoms are used to show a vector (the surface
point and the normal at the point); they have no chemical meaning.

You can concatenate molsurfpdb.pdb and your lipid.pdb to see they are
correctly aligned.

If your forces are OK but your hole is still closing up, you must have
the force constant hfm too small. (And you have got pressure coupling
switched on, haven't you?) Keep increasing it until the hole starts
widening instead. You shouldn't need to do a whole ns to see what's
happening here - a hundred ps should be enough.


Rob Yang wrote:

Thank you Dr. G, Smith. I fixed the problem in lipids jumping around,
was able to obtain 1 ns of md (make_hole version) for the membrane with
hole alone. The membrane seemed to be stable as the bilayer stayed where

they were supposed to this time and boy did I ever enjoy the trajectory
movie. However, upon further inspection, the hole had "sealed up" at the
of the simulation.  The hole I created using the make_hole.pl before
the md had been filled by surrounding lipids. This led me to think that
maybe the exclusion forces of the protein surface are not correct (could
due to user error on my part when using MSMS?). I examined the
insidesurf.pdb and molsurfpdb.pdb using vmd and couldn't figure out what
should be looking for.

So my questions are:
1) How can I use the information of insidsurf.pdb and molsurfpdb.pdb
perhaps gsurf.log) to convince myself that the calculated forces are
"reasonable".  In the tutorial it says that the forces of the
should be pointing outward at the right residues, but I couldn't see any

directions.  I.e, what would be a sanity test here?
2) Any other reasons why the hole grew back together?


Dr Graham R. Smith
Biosystems Informatics Institute
Newcastle upon Tyne

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