Help pls: Got error on FEP calculation: ERROR: The following variables are NOT VALID lambda2...

From: Li, Hongzhi (holi_at_coh.org)
Date: Mon Nov 09 2009 - 12:18:59 CST

Hello,

It was my first time to run FEP free energy calculation by following the tutorial. I always got the ERROR message at equilibrium or MD run even with the newest version I downloaded today (either nomal V2.7b1 or cuda-enabled):
(I would appreciate if anyone can help me here)

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE

Charm++ fatal error:
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE

Info: Running on 1 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00420022 s
Info: 1.50328 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is fep_wb.cfg
TCL: Running FEP window 1: Lambda1 0.0 Lambda2 0.0000001 [dLambda 1e-07 ]
TCL: Suspending until startup complete.
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: lambda2
ERROR: lambda
ERROR: fepEquilSteps
ERROR: fepOutFreq
ERROR: fepOutFile
ERROR: fepCol
ERROR: fepFile
ERROR: fep
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE

Here is my command line: ~/NAMD_CVS_Linux-x86_64/namd2 +idlepoll fep_wb.cfg
My fep.tcl is copied from tutorial.
Here is my conf file:
###################################################
# ALCHEMICAL TRANSFORMATION
###################################################
# INPUT
parameters par_all22_prot.inp
paraTypeCharmm on
exclude scaled1-4
1-4scaling 1.0

# TOPOLOGY
structure solvate.psf

# COORDINATES
coordinates equilibrate_0.coor
bincoordinates equilibrate.coor

# VELOCITIES
velocities equilibrate_0.vel
binvelocities equilibrate.vel

# CELL
extendedSystem equilibrate.xsc

# OUTPUT FREQUENCIES
outputenergies 100
outputtiming 100
outputpressure 100
restartfreq 100
XSTFreq 100

# OUTPUT AND RESTART
outputname alchemy_0
restartname alchemy
binaryoutput no
binaryrestart yes

# PME
PME yes
PMETolerance 10e-6
PMEInterpOrder 4
PMEGridSizeX 36
PMEGridSizeY 36
PMEGridSizeZ 36

# WRAP WATER FOR OUTPUT
wrapAll on

# CONSTANT-T
langevin on
langevinTemp 300.0
langevinDamping 1.0

# CONSTANT-P
LangevinPiston on
LangevinPistonTarget 1
LangevinPistonPeriod 100
LangevinPistonDecay 100
LangevinPistonTemp 300
StrainRate 0.0 0.0 0.0
useGroupPressure yes
useflexiblecell no

# SPACE PARTITIONING
splitpatch hydrogen
hgroupcutoff 2.8
stepspercycle 20
margin 1.0

# CUT-OFFS
switching on
switchdist 8.0
cutoff 9.0
pairlistdist 10.0

# RESPA PROPAGATOR
timestep 1.0
fullElectFrequency 4
nonbondedFreq 2

# SHAKE
rigidbonds all
rigidtolerance 0.000001
rigiditerations 400

# COM
commotion no

# FEP
source fep.tcl
fep on
fepFile solvate.fep
fepCol B
fepOutFile alchemy.fepout
fepOutFreq 1

# LOOP OVER LAMBDA-STATES
fepEquilSteps 2000
set nSteps 10000
set dLambda 0.1
set init {0.0 0.0000001 0.000001 0.00001 0.0001 0.001 0.01 0.05 0.1}
set end {0.9 0.95 0.99 0.999 0.9999 0.99999 0.999999 0.9999999 1.0}
runFEPlist $init $nSteps
runFEP 0.1 0.9 $dLambda $nSteps
runFEPlist $end $nSteps

Best regards,

Hogan

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