[gmx-users] Invalid atom number 101717 in indexfile

Natalie Stephenson Natalie.Stephenson at postgrad.manchester.ac.uk
Fri Dec 10 13:18:05 CET 2010


Hi,

I've come across this error when performing grompp of my pull files before an afm simulation.  I'm not really sure I understand why it's saying it ... I've checked over my index file and the atom is part of the solvent I've solvated the box with during genbox commands.

The input on the grompp I performed was ...
grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.trr -o pull.tpr
which produced the error below ...

-------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: readir.c, line: 1371

Fatal error:
Invalid atom number 101717 in indexfile
-------------------------------------------------------
What is it I'm doing wrong?! :-S I'm not even really sure where the error lies with this one? Is it a step I've performed earlier that's incorrect?  Can I just remove this atom from the index file and hope for the best?

Thanks loads
Natalie


mdp file I used is below ...

title        = Umbrella pulling simulation
define        = -DPOSRES_B
; Run parameters
integrator    = md
dt        = 0.001
tinit        = 0
nsteps        = 5000000    ; 10 ns
nstcomm        = 1
; Output parameters
nstxout        = 50000        ; every 100 ps
nstvout        = 50000
nstfout        = 5000
nstxtcout    = 5000        ; every 10 ps
nstenergy    = 5000
; Bond parameters
constraint_algorithm     = lincs
constraints        = all-bonds
continuation         = yes        ; continuing from NPT
; Single-range cutoff scheme
nstlist        = 5
ns_type        = grid
rlist        = 1.4
rcoulomb    = 1.4
rvdw        = 1.4
; PME electrostatics parameters
coulombtype    = PME
fourierspacing  = 0.12
fourier_nx    = 0
fourier_ny     = 0
fourier_nz    = 0
pme_order    = 4
ewald_rtol    = 1e-5
optimize_fft    = yes
; Berendsen temperature coupling is on in two groups
Tcoupl         = Nose-Hoover
nsttcouple    = -1
tc_grps        = Protein Non-Protein
tau_t        = 0.1 0.1
ref_t        = 310 310
; Pressure coupling is on
Pcoupl        = Parrinello-Rahman
pcoupltype    = isotropic
tau_p        = 1.0
compressibility    = 4.5e-5
ref_p        = 1.0
; Generate velocities is off
gen_vel        = no
gen_temp    = 310
gen_seed    = 1
; Periodic boundary conditions are on in all directions
pbc        = xyz
; Long-range dispersion correction
DispCorr    = EnerPres
; Pull code
pull        = umbrella
pull_geometry    = distance    ; can't get PMF with direction
pull_dim    = N N Y
pull_start    = yes
pull_ngroups    = 1
pull_group0    = C-Terminal
pull_group1    = N-Terminal
pull_init1    = 0
pull_rate1    = 0.005
pull_k1        = 1500        ; kJ mol^-1 nm^-2
pull_nstxout    = 1000        ; every 2 ps
pull_nstfout    = 1000        ; every 2 ps
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