FATAL ERROR: Unable to open extended system file.

From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Mon Jul 30 2007 - 02:27:49 CDT

Hi Folks,

I am trying to do an MD simulation for a simple test example using
ubiquitin. I first do an energy minimization, followed by heating to 300K.
After this, when I try to do an equilibration run, I get the error:

FATAL ERROR: Unable to open extended system file.

My equilibration config file looks like this:

######################TOSET############################
# molecular system
set MOL 1UBQ_PandS_wb
structure ${MOL}.psf

# after heating.
set inprot ${MOL}_heat
coordinates ${inprot}.coor
velocities ${inprot}.vel
extendedSystem ${inprot}.xsc

set temperature 300 ;# the temperature

set outputname ${MOL}_eq
set eq_restart ${MOL}_eq_restart

firsttimestep 0 ;# reset to 0 for equilibration run.

fixedAtoms off

# force field
paratypecharmm on
parameters ../topology_files/toppar/par_all22_prot.inp
exclude scaled1-4
1-4scaling 1.0

cellBasisVector1 72.165 0.0 0.0
cellBasisVector2 0.0 74.867 0.0
cellBasisVector3 0.0 0.0 77.663
cellOrigin 30.5597000122 30.3731307983 17.1436786652
wrapAll on

PME on
PMEGridSizeX 75 # size along cellBasisVector1.
PMEGridSizeY 75 # along cellBasisVector2.
PMEGridSizeZ 80
# use numbers with small integer factors: 2,3,5.

# approximations
switching on
switchdist 10
cutoff 12
pairlistdist 13.5

# center-of-mass motion is automatically removed.

# integrator
timestep 1.0 ;# in fs.
stepspercycle 20 ;# default
nonbondedFreq 2 ;# same as BerendsenPressureFreq

fullElectFrequency 2

# output
outputName $outputname
dcdfreq 1000 ;# every ps
xstFreq 1000
outputEnergies 1000
outputPressure 1000
outputtiming 1000
binaryoutput no

# for restarting:
restartname $eq_restart
restartfreq 10000
restartsave yes
binaryrestart no ;# yes will preserves more accuracy.

# Temperature coupling via Langevin dynamics.
langevin on
langevinTemp $temperature
langevinDamping 1.0 ;# from mailing-list

langevinHydrogen on

# Pressure coupling by Nose-Hoover Langevin piston pressure control
LangevinPiston on
LangevinPistonTarget 1.01325 ;# in bar.
LangevinPistonPeriod 200 ;# in fs.
LangevinPistonDecay 100
LangevinPistonTemp $temperature ;# set same as langevinTemp.

# GPressure seems to fluctuate about 1.0, betw -2K to 2K.

useGroupPressure yes # use hydrogen-group based virial. use with rigidBonds.

# GROMACS: ref_p = 1.0 bar; compressibility = 4.5e-5 bar-1; tau_p = 0.5 ps
# but tau_p = 0.1ps gave errors.

margin 3.0 ; # increase margin to overcome problem with
decreasing cell size.

# to use SHAKE to constraint all bonds during free MD only.
rigidBonds all

# short equilibration run
run 50000 ; # 50 ps

Has anyone come across this error before. Or can anyone spot some obvious
problem with my configuration file?

Thanks,

Arun

-- 
***********************************************
Arun Krishnan, Ph.D,
Assistant Professor,
Institute for Advanced Biosciences,
Keio University,
Center Building,
Tsuruoka, Yamagata 997-0035
Japan
Phone: +81 (0)235-29-0824
Email: krishnan_at_ttck.keio.ac.jp
URL: http://www.iab.keio.ac.jp/~krishnan
**********************************************

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