[gmx-users] Position-restraint

[XAvier Periole]

On Jul 28, 2009, at 9:50 AM, Morteza Khabiri wrote:

> 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
> message:
>
> 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)
The erro is here and has been pointed out to you already. your posre  
file
contains more position restraints than atoms!
>
> 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"
> #endif
>
> #include "ligand.itp"
>
> #ifdef POSRES_LIGAND
> #include "ligand_posre.itp"
> #endif
>
> #include "spc.itp"
>
> (etc).
>
> 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"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>   1    1       1000       1000       1000
> #endif
>
> ; 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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