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
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