[gmx-users] Position-restraint

Morteza Khabiri khabiri at greentech.cz
Tue Jul 28 09:50:41 CEST 2009

Dear gmx-users,

I am trying to create a tpr file using grompp.  My system has a protein with
four identical chains, 288 POPC molecules, SOL, and ions.  I am trying to
restrain the lipid molecules.  When running grompp, I get the following

Program grompp, VERSION 3.3
Source code file: toppush.c, line: 1108

Fatal error:
[ file "posre_entirelipid1.itp", line 56 ]:
            Atom index (53) in position_restraints out of bounds (1-52)

I sent an email about this yesterday, but the advice was not applicable
because of the set-up of my topology file.

previous advice:  **********************
Position restraints sections must be placed within the same [ moleculetype ]
definition. So, you can't include all of the position restraint information
in one file, since that file is part of the Protein [ moleculetype ]
definition. The ligand should be placed in its own posre.itp file and
included in the topology.

These lines must be placed *outside* of the [ moleculetype ] directive of
any other molecule(s) in the system. For consistency, whenever I have
ligands, I place them immediately after the protein [ moleculetype ] and
water topology, i.e.:

#ifdef POSRES
#include "posre.itp"

#include "ligand.itp"

#include "ligand_posre.itp"

#include "spc.itp"


That way, the protein [ moleculetype ] ends with the #ifdef POSRES, the
ligand section begins with #include "ligand.itp", ends with the
POSRES_LIGAND section, and then the topology reads the water topology, etc.

This is the structure of my main topology file:

; Include forcefield parameters
#include "ffoplsaa.itp"

; Include chain topologies
#include "topol_A.itp"
#include "topol_B.itp"
#include "topol_C.itp"
#include "topol_D.itp"

; Include lipid topology
#include "popc_Stockner.itp"

; Include water topology
#include "spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
Protein_C           1
Protein_D           1
POPC              288
SOL              33722
NA+               28


At the end of the lipid topology file popc_Stockner.itp, I have placed the
#include for the lipid position restraint file posre_lipid.itp.   I tried
moving the #include for the lipid position restraint into the main topology
file, directly after the include lipid topology line, but this gives me the
same error.

Do you have any suggestions of where exactly to put the #include for the
lipid position restraint?

Thank you very much
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