[gmx-users] Teethering/ Fatal error when using posre
Joanne Hanna
J.F.Hanna at warwick.ac.uk
Thu May 19 15:47:09 CEST 2005
Sorry!
Okay i understand i need to write 5 nos!
Joanne Hanna
Department of Chemistry
University of Warwick
Coventry
CV4 7AL
J.F.Hanna at warwick.ac.uk
jfhanna at gmail.com
>>> J.F.Hanna at warwick.ac.uk 05/19/05 14:41 PM >>>
Thank you, i understand this now.
Do you have any suggestions what this error is in relation to?
processing index file...
Fatal error: Not enough annealing values: 1 (for 5 groups)
this is my *.mdp file and i have defined no annealing.
;
; File 'mdout.mdp' was generated
; By user: bond (386)
; On host: torpedo.biop.ox.ac.uk
; At date: Sun Nov 18 20:52:58 2001
;
; VARIOUS PREPROCESSING OPTIONS =
title = Enzyme Plus Lig Solv plus Ion PosRes MD
cpp = /lib/cpp
;include =
define = -DPOSRES
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0
dt = 0.002
nsteps = 250000
; number of steps for center of mass motion removal =
nstcomm = 1
; groups for center of mass motion removal - default is whole system =
comm-grps =
; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
bd-temp = 310
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol = 100
emstep = 0.01
; Max number of iterations in relax_shells =
niter = 0
; Frequency of steepest descents steps when doing CG =
nstcgsteep = 1000
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 100
nstvout = 100
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 500
xtc-precision = 500
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps = PROTEIN LIG MG2+ AMP SOL NA+
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns-type = Grid
; Periodic boundary conditions: xyz or no =
pbc = xyz
; nblist cut-off =
rlist = 1.0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r = 1
; Method for doing Van der Waals =
vdw-type = Cut-off
; cut-off lengths =
rvdw-switch = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters =
pme_order = 4
ewald_rtol = 1e-05
epsilon_surface = 0
optimize_fft = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling - no,berendsen,nose-hoover =
tcoupl = berendsen
; Groups to couple separately =
tc-grps = PROTEIN LIG MG2+ AMP SOLVENT
tau-t = 0.5 0.5 0.5 0.5 0.5
ref-t = 310 310 310 310 310
; Pressure coupling - no,berendsen,parinello-rahman =
Pcoupl = no
; Pressure coupling type - isotropic,semiisotropic,anisotropic,surface-tension,triclinic
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau-p = 5.0 5.0
compressibility = 4.5E-5
ref-p = 1.0 1.0
; SIMULATED ANNEALING CONTROL =
annealing = no
; Time at which temperature should be zero (ps) =
;zero-temp_time = 0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen-vel = yes
gen-temp = 310
gen-seed = 173529
; OPTIONS FOR BONDS = lincs
constraints = all-bonds
; Type of constraint algorithm =
constraint-algorithm = Shake
; Do not constrain the start configuration =
unconstrained-start = yes
; Relative tolerance of shake =
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials =
morse = no
; ENERGY GROUP EXCLUSIONS =
; Useful for excluding interactions within frozen groups
; Pairs of energy groups for which all non-bonded interactions are excluded
; E.g. Protein Protein SOL SOL - only non-bonded interactions between protein+solvent =
energygrp_excl =
; NMR refinement stuff =
; Distance restraints type: No, Simple or Ensemble =
disre = No
; Force weighting of pairs in one distance restraint: Equal or Conservative =
disre-weighting = Equal
; Use sqrt of the time averaged times the instantaneous violation =
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file =
nstdisreout = 100
; Free energy control stuff =
free-energy = no
init-lambda = 0
delta-lambda = 0
sc-alpha = 0
sc-sigma = 0.3
>>> spoel at xray.bmc.uu.se 05/19/05 13:31 PM >>>
On Thu, 2005-05-19 at 12:40 +0100, Joanne Hanna wrote:
> Hi
>
> I am getting this error when trying to grompp my files:
> Fatal error: [ file "posre_lig.itp", line 5 ]:
> Atom index (5214) in position_restraints out of bounds (1-20)
>
> I do not know what this means or how to fix it, i have generated my posre files for my protein and three ligands using genpr. these are defined in the *.top files by using an ifdef statement and in the *.mdp i have defined -DPOSRES.
>
your include statement for posres is in the wrong molecule definition.
not in the protein but in some other 20 atom molecule.
chpater 5 in the manual.
> can anybody help point me in the right direction?
>
> Thanks
> Jo
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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