[gmx-users] Making holes in lipid bilayers membranes

[Graham Smith]

Hi folks 


A couple of people have asked me and/or Jose Faraldo-Gomez for the
code for the modified version of mdrun that can be used to make a hole
in a lipid bilayer that is the right shape to insert the membrane
protein of your choice. It does this by reading a molecular surface
file made by Grasp or MSMS.  (Faraldo-Gomez, Smith and Sansom,
Eur. Biophys J (2002) 31:217-227). Extra parameters are set in 
a command-line mdp file read by mdrun.

I have now uploaded to the Contributions page a tar file containing
code for an updated version of this, based on gromacs 3.1.4
(previously it was based on version 2.0).

1. installation

##### warning! ###### It will replace the existing mdrun and some
source files, so don't extract it into your "main" copy of the
distribution, make a separate copy of the gromacs source distribution
before unpacking it. 

you should be in the main gmx directory when you unpack, i.e. if you
do ls
you see

acinclude.m4  config/	    include/	 man/
share/
aclocal.m4    configure*    INSTALL	 mdrun_make_hole.tar.gz  src/
admin/	      configure.ac  Makefile.am  README
AUTHORS       COPYING	    Makefile.in  scripts/

Unpack with 

gunzip -c mdrun_make_hole.tar.gz |tar -xv 

then make in the usual way. 

2. use. 

For instructions on how to use the program, look at 

share/tutor/make_hole/gsurfaceexpl.html

which is a reasonably complete manual. 

Cheers, 

-Graham




########################################################################

Dr. Graham R. Smith, 		       Department of Biological Sciences,  
Biomolecular Modelling Laboratory,     Biochemistry Building,              	
Cancer Research UK, 		       Imperial College of Science,        	
44 Lincoln's Inn Fields, 	        Technology & Medicine,             	
London WC2A 3PX,		       London SW7 2AZ,                     	
U.K. 				       U.K.                                	
Tel: +44-(0)20 7269 3348 	       Tel: +44-(0)20 7594 5737            	
email: graham.smith at cancer.org.uk	
URL: http://www.bmm.icnet.uk/~smithgr