[gmx-users] position restraint problem!

[nanyu101 at sina.com]

Dear gmx-users,
 
   I have four groups to restraint in my simulation. The first is dppc bilayer, second is ion channel, the third is calcium cation and the last is chloride anion. I have tried two methods just as gmx-users told, but I failed both in restrainting the ions.
   The first methods listed as following:
1.my grompp.top file:
include forcefield parameters
#include "ffG43a2.itp"
#include "dpp.itp"
#include "posre_dpp.itp"
#include "phb.itp"
#include "posre_phb.itp"
#include "ions.itp"
#include "posre_ion.itp"

In the posre_dpp.itp has 50 atoms' restraint, the posre_phb.itp is from running pdb2gmx -f ion.pdb -o ion.gro -p ion.top -i posre_phb.itp. These two restraint files run normally. The posre_ion.itp file has two conformation. First method includes the atom number of the ions:
; position restraints for CA2 of 

[ position_restraints ]
;  i funct       fcx        fcy        fcz
6169    1       10000       10000       10000
6170    1       10000       10000       10000
6171    1       10000       10000       10000
6172    1       10000       10000       10000
6173    1       10000       10000       10000
6174    1       10000       10000       10000
6175    1       10000       10000       10000
6176    1       10000       10000       10000
6177    1       10000       10000       10000
6178    1       10000       10000       10000
6179    1       10000       10000       10000
6180    1       10000       10000       10000
6181    1       10000       10000       10000
6182    1       10000       10000       10000
6183    1       10000       10000       10000
6184    1       10000       10000       10000

The second is include only one:
; position restraints for CA2 of 

[ position_restraints ]
;  i funct       fcx        fcy        fcz
1    1       10000       10000       10000

   No matter how I have tried, the ions can't been restraint in my simulation.. The most commonly errors is like the following information:

Fatal error: [ file "posre_dpp.itp", line 6 ]:
             Atom index (2) in position_restraints out of bounds (1-1)



   Would you please give me some advices? many thanks.

Best wishes,
nanyu

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