[gmx-users] a problem with grompp

[Mark Abraham]

On 23/01/2012 10:13 PM, Banafsheh Mehrazma wrote:
> Dear all;
> I am trying to constrain a double stranded DNA, I have made an index
> file and a posre.itp file, and then when I wanted to run grompp
> command I have encountered this:
> ...........................................
> Program grompp, VERSION 4.5.3
> Source code file: toppush.c, line: 1526
>
> Fatal error:
> [ file posre_DNA.itp, line 318 ]:
> Atom index (314) in position_restraints out of bounds (1-313).
> 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.

This is very likely to be literally what's wrong.

> ...........................................................................
>
> and the following lines are some parts of my .mdp file;
> ......................................................................................
> title		= DNA NVT equilibration
> define		= -DPOSRES_DNA	; position restrain the DNA
> ; Run parameters
> integrator	= md		; leap-frog integrator
> nsteps		= 75000		; 2 * 75000 = 150 ps
>
> ; Temperature coupling is on
> tcoupl		= V-rescale	; modified Berendsen thermostat
> tc-grps		= DNA   Water_and_ions
> tau_t		= 0.1 	0.1		; time constant, in ps
> ref_t		= 310 	310		
> .........................................................................................
>   and my topl.top is the following lines;
>
>
>
> ; Include forcefield parameters
> #include "amber99.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "topol_DNA_chain_A.itp"
> #include "topol_DNA_chain_B.itp"
>
> #ifdef POSRES_DNA
> #include "posre_DNA.itp"
> #endif

Each [position_restraints] section can pertain only to the immediately 
foregoing [moleculetype], per the above error message. Break it up or 
move it accordingly.

Mark

>
> ; Include water topology
> #include "amber99.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "amber99.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein in water
>
> [ molecules ]
> ; Compound        #mols
> DNA_chain_A         1
> DNA_chain_B         1
> SOL         5580
> NA          18
>
> ..............................................................................................
>
>
> what do you suggest that I do to make it work?
> Thank you
> B.Mehrazma