nur avneet wrote:
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?
Table 5.4 in the manual.
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..
That means you're trying to restrain atom number 8 in a molecule that
has only 3 atoms. Read section 5.6.1 to work out how you managed to do this.
Mark
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