[gmx-users] Problem in starting make hole

nur avneet nuravneet at yahoo.co.in
Thu Nov 22 12:19:19 CET 2007

 i want to use makehole program (gromacs 3.1.4)and i used the grompp command on dmpc.pdb with position restraints as specified in the tutorial.
 the position restraint file is as follows :
 [ position_restraints ]
 ; atom  type      fx      fy      fz
      8     1     0.0     0.0  1000.0
 the tutorial says, this will restraint all phosphorous atoms in the bilayer in z-coordinates.
 What does "type" specify? also, the pdb file has different number for every phosphorous atom of the dmpc molecules. Will specifying only '8' only , restraint all P8s? 
 when i give the grompp command i get the following error:
 Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
 checking input for internal consistency...
 calling /lib/cpp...
 cecmel311334_hole_dmpc.top:11:1: error: unterminated #else
 cpp exit code: 256
 Tried to execute: '/lib/cpp  -I/usr/local/gromacs/share/top -DPOSRES cecmel311334_hole_dmpc.top > gromppZOiO4o'
 The '/lib/cpp' command is defined in the .mdp file
 processing topology...
 Generated 1174 of the 2016 non-bonded parameter combinations
 Cleaning up temporary file gromppZOiO4o
 Fatal error: [ file "lipid_posre.itp", line 3 ]:
              Atom index (8) in position_restraints out of bounds (1-3)
 What does this mean? n please guide how to proceed..
 due regards
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