[gmx-users] Invalid atom number 101717 in indexfile

Sun Dec 12 14:21:25 CET 2010

Thanks for spotting that! I'd thought the system was complete when I'd done the index file - had completely forgot that I'd then gone onto generating ions! 

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 13:52
To: Gromacs Users' List
Subject: Re: [gmx-users] Invalid atom number 101717 in indexfile

Natalie Stephenson wrote:
> 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)
>

But then you added ions?  You should make your .ndx file only after the system
is complete, otherwise, if you've replaced a water molecule with an ion, the
atom index for that atom will belong to a different group.

-Justin

> 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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--
========================================

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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