[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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