[gmx-users] Invalid atom number 101717 in indexfile

[Natalie Stephenson]

Hi,

There are 101987 atoms in my system (2206 from my protein and the rest from solvent and ions).  The index file was made with make_ndx
after creating the solvated box
Command used was "make_ndx -f solv.gro" (solv.gro being the output from genbox)

Natalie
xxx

________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 10 December 2010 12:26
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Invalid atom number 101717 in indexfile

Natalie Stephenson wrote:
> 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?
>

Never make ad hoc changes to any file that Gromacs produces unless you know the
consequences of doing so.  If make_ndx wrote that atom number, it did so for a
reason.

How many atoms are in your system?  How did you create the .ndx file?

-Justin

> 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
>

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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