fatal error: tried to assign bond index before all parameter files were read

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Wed May 06 2009 - 05:36:16 CDT

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Hi all,

I am getting this error while trying to execute my input file

fatal error: tried to assign bond index before all parameter files were read

I have not encountered this error before my input file looks like

# set PDB and PSF file
set pdb fr.inpcrd.pdb

amber on
parmfile fr.prmtop
ambercoor fr.inpcrd

set temperature 300

# Set number of minimization steps
set min 10000

# Set number of MD steps
set md 0

# Freezing atoms for minimization
set fix 1
set pme 0
set nve 0
set npt 0

#################################
# Adjustable parameters
#################################

outputName met_water

##################################

restartfreq 500
# 500 steps = every 1ps
dcdfreq 2000
xstFreq 500

outputEnergies 100
# 100 steps - every 0.2 ps
outputTiming 1000

# Shows time per step and time to completion

firsttimestep 0

#################################
# Simulation parameters
#################################

# Input
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.8333
# Cutoff is increased during minimisation
cutoff 16.
switching on
switchdist 14
# Switchdist = Cutoff - 2

# Promise that atom will not move more than 2A in a cycle
pairlistdist 18
# Cutoff + 2
stepspercycle 10
# Redo pairlists every ten steps

# Integrator Parameters
timestep 0.5
# 0.5 fs/step
rigidBonds all
# needed for 2fs steps
nonbondedFreq 1
# nonbonded forces every step
fullElectFrequency 2
# PME only every other step

###################################
#
# Temperature and Pressure control
#
###################################
###################################
#
# Constant Temperature Control
#
###################################

if {$nve==1} {
langevin on
# langevin dynamics
langevinDamping 5.
# damping coefficient of 5/ps
langevinTemp $temperature
# Random noise at this level
langevinHydrogen no
# Do not couple bath to hydrogens
}
####################################
#
#
# Pressure Control
#
#
####################################

if {$npt == 1} {
langevinPiston on
# Appling the langevinpiston for pressure control
langevinPistonTarget 1.01325
# One atomsheric pressure at sea level
langevinPistonPeriod 100
# barostat oscillation time scale for LP method
langevinPistonDecay 50
# barostat damping time scale for LP
LangevinPistonTemp $temperature
# barostat noise temperature for LP

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigid bonds
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, maybe for membrane
}
######################################
# Fixing the protein for equilibration
# with the water
######################################
if {$fix==1} {
        fixedatoms on
        fixedatomscol B
}

# Periodic Boundary conditions

##cellBasisVector1 $x 0. 0.
# Vector next to image
##cellBasisVector2 0. $y 0.
##cellBasisVector3 0. 0. $z
##cellOrigin $x0 $y0 $z0

wrapWater on
wrapAll on

# Particle Mesh Ewald

if {$pme == 1} {
   PME yes
   PMEGridSizeX 64 ;# 3^2*2^3, close to 71.2
   PMEGridSizeY 64 ;# 2^3*3^2 , close to 71.37
   PMEGridSizeZ 64 ;# 2^7, close to 117.47
}

# the center of the cell

minimize $min
# lower potential energy for 1000 steps
reinitvels $temperature

run $md

Any hint appreciated thanks in advance

Best

Jorgen

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