Sir
 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
 nur
 
       
---------------------------------
 Chat on a cool, new interface. No download required. Click here.
_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to