[gmx-users] mdrun_make_hole

Itamar Kass ikass at mail.ls.huji.ac.il
Tue Jan 28 22:18:00 CET 2003

  Dear smarter people, I am trying to us the modified mdrun_make_hole
contributed by Dr. Graham R. Smith.  Because I do not have MSMS nor GRASP, I
tried to make a cylindrical hole.  As a first step I downloaded dmpc_npat.pdb
from Dr. Peter Tieleman homepage, but the script make_hole.pl made nothing to
the file - no hole could be seen.  When I tried to keep on, the same had happen,
mdrun made no hole within the bilayer. 
   My first question deals with the pdb file; the DMPC molecules are written as
DMP,  will GROMACS recognize them when I write  #include "dmpc.itp" or should I
write in the file DMPC?  The second question is regarding the  script, do I have
to cast a spell upon the computer before running the script or did I do
something wrong?  My last question is are their any international workshop
regarding GROMACS in which such methods can be taught?
   "Toda" - Thanks you all, Itamar.

Computers are like airconditioners... They don't work well with Windows open.

| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585146
| Fax: +972-(0)2-6584329
| Email: ikass at vms.huji.ac.il
| Group Homepage: http://www.ls.huji.ac.il/~membranelab/

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