[gmx-users] position restraint problem!

[Martina Bertsch, PhD]

Your syntax is interpreted as trying to restrain atom 2 in a molecule that has only one atom. 

The position restraints are molecule-based, therefore they must appear inside the proper [ molecule_type ] subsection in the .top file. 
E.g., in your protein.top file, at the end of the listing of all atoms, bonds, angles and dihedrals, you will find:

; Include position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

Also, at the end of the listing of atoms, bonds, etc. in the dppc.itp, you will find:

#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif

Similarly, the ions.itp file contains a [ molecule_type ] section for each of the separate ions, after which you should
insert the posres statement.

Of course, if you are using ifdef/endif, the *posre.itp will only be included if the *mdp file defines the appropriate posres.

Best,

Martina Bertsch, Ph.D.
Northwestern University
Feinberg School of Medicine
Molecular Pharmacology and Biological Chemistry
303 East Chicago Avenue
Chicago, IL 60611


nanyu101 at sina.com wrote:

>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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