[gmx-users] Problem with multiple Urea molecule position restraining.

[Mark Abraham]

karan syal wrote:
> Dear All,
> 
> I am trying to do equilibration of 8M urea in gromacs 4.0 in a 3nm cubic
> box. I created posre.itp from genpr selecting only UREA atoms to be
> restrainted ( em.gro was used to generate this posre.itp)
> 
> *The error message is given below :*
> 
>  grompp -f pr.mdp -c em3.gro -p sys.top -o pr.tpr
> 
>                          :-)  G  R  O  M  A  C  S  (-:
> 
>                       GROwing Monsters And Cloning Shrimps
> 
>                              :-)  VERSION 4.0  (-:
> 
> 
>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2008, The GROMACS development team,
>             check out http://www.gromacs.org for more information.
> 
>          This program is free software; you can redistribute it and/or
>           modify it under the terms of the GNU General Public License
>          as published by the Free Software Foundation; either version 2
>              of the License, or (at your option) any later version.
> 
>                                 :-)  grompp  (-:
> 
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f         pr.mdp  Input, Opt!  grompp input file with MD parameters
>  -po      mdout.mdp  Output       grompp input file with MD parameters
>   -c        em3.gro  Input        Structure file: gro g96 pdb tpr tpb tpa
>   -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>  -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>   -n      index.ndx  Input, Opt.  Index file
>   -p        sys.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o         pr.tpr  Output       Run input file: tpr tpb tpa
>   -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e       ener.edr  Input, Opt.  Energy file: edr ene
> 
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -nice        int    0       Set the nicelevel
> -[no]v       bool   yes     Be loud and noisy
> -time        real   -1      Take frame at or first after this time.
> -[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
>                             sites
> -maxwarn     int    0       Number of allowed warnings during input
> processing
> -[no]zero    bool   no      Set parameters for bonded interactions without
>                             defaults to zero instead of generating an error
> -[no]renum   bool   yes     Renumber atomtypes and minimize number of
>                             atomtypes
> 
> Ignoring obsolete mdp entry 'cpp'
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs4/share/gromacs/top/ffG43a1.itp
> Opening library file /usr/local/gromacs4/share/gromacs/top/ffG43a1nb.itp
> Opening library file /usr/local/gromacs4/share/gromacs/top/ffG43a1bon.itp
> Opening library file /usr/local/gromacs4/share/gromacs/top/ff_dum.itp
> Opening library file /usr/local/gromacs4/share/gromacs/top/spc.itp
> Generated 279 of the 1225 non-bonded parameter combinations
> 
> *-------------------------------------------------------
> Program grompp, VERSION 4.0
> Source code file: toppush.c, line: 1196
> 
> Fatal error:
> [ file posre.itp, line 13 ]:
> Atom index (9) in position_restraints out of bounds (1-8).
> This probably means that you have inserted topology section
> "position_restraints"
> in a part belonging to a different molecule than you intended to.
> In that case move the "position_restraints" section to the right molecule.
> -------------------------------------------------------
> *
> 
> *My top file is : *
> 
> ;       This is your topology file
> ;       UREA in Water t=   0.00000
> ;
> ; Include forcefield parameters
> #include "ffG43a1.itp"
> 
> #include "spc.itp"
> #include "urea.itp"
> 
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> 
> 
> 
> [ system ]
> ; Name
> UREA in Water
> 
> [ molecules ]
> ; Compound        #mols
> UREA               130
> SOL               1149
> 
> 
> 
> I *guess* the error is because position restraints for all the 130 urea
> molecules is not working but only for the first molecule of UREA.  ( Hence
> out of bounds after 1-8.)
> 
> Can anyone please suggest a way out of this problem? i want to position
> restrain all the urea molecules.

The [ position_restraints ] directive applies per-molecule, like all the 
other [ moleculetype ] sub-directives. Just restrict it to the atoms 
that you've defined in the [ atoms ] sub-directive of the urea [ 
moleculetype ]

Mark