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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@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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