[gmx-users] flat-bottom reference file format

[Jinmei Wang]

dear list,

I want to restrain a group of atoms within one sphere. I got the sphere
center coordinate using g_traj

In topol.top I added this part:

#ifdef POSRES_FLATBOTTOM
[ position_restraints ]
;  i funct       g        r(nm)        k (kJ/mol/nm)
   4    2        1        1.5          300000
 857    2        1        1.5          300000
1715    2        1        1.5          300000
#endif

and in the reference file I put:

ATOM      4  CA  GLY   704      21.698  27.798   9.333  1.00  0.00
  C
ATOM   857  CA  GLY   704      21.698  27.798   9.333  1.00  0.00
C
ATOM 1715  CA   GLY   704      21.698  27.798   9.333  1.00  0.00
C

but I came across this error:

WARNING 1 [file topol.top, line 16661]:
 The number of atoms in flat.pdb (3) does not match the number of atoms in
the topology (97123). Will assume that the first 3 atoms in the topology
and flat.pdb match.

could anybody tell me what's wrong with my -r file? it goes well without
giving reference file.

thanks in advance.
Jinmei