From: roberta.rostagno (roberta.rostagno_at_unimib.it)
Date: Mon May 11 2009 - 07:38:38 CDT
Dear all,
I'm e new namd user. I would like to perform a
minimization and MD on e protein+ligand+water system with
AMBER imput files
My conf file is:
amber yes
parmfile M52SKIresp.prmtop
ambercoor M52SKIresp.prmcrd
readexclusions off
outputname 1M52SKIrespsimulatedannealing
restartName 1m52SKIrespsimannrest
set temperature 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
temperature $temperature
# Periodic Boundary conditions
# NOTE: Do not set the periodic cell basis if you have
also
# specified an .xsc restart file!
if {0} {
cellBasisVector1 88. 0. 0.
cellBasisVector2 0. 88 0.
cellBasisVector3 0. 0 88.
cellOrigin -0.00 -0.16 0.26
}
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.833333
cutoff 12.
switching on
switchdist 10.
pairlistdist 14.0
# Integrator Parameters
timestep 0.5;# 1 fs/step
numsteps 23624000
rigidBonds all ;# needed for 2fs steps
rigidTolerance 0.0005
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
#PME (for full-system periodic electrostatics)
if {0} {
PME yes
PMEGridSizeX 90
PMEGridSizeY 90
PMEGridSizeZ 90
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to
hydrogens
# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 100
langevinPistonTemp $temperature
}
restartfreq 200 ;# 500steps = every 1ps
dcdfreq 100
outputEnergies 100
outputPressure 100
dcdfile 1m52SKIrespsimann.dcd
# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms on
fixedAtomsFile fix.pdb
fixedAtomsCol B
}
constraints on
consRef restrain.pdb
consKFile restrain.pdb
consKCol B
#############################################################
## EXECUTION SCRIPT ##
#############################################################
langevinpiston off
Minimization on
if {0} {
minimize 20000
reinitvels $temperature
}
fixedatoms off
langevinpiston on
reassignFreq 2000
reassignTemp 0
minimize 2000
for { set TEMP 0 } {$TEMP<601} {incr TEMP 1} {
reassignTemp $TEMP
run 2000
}
run 1000000
for { set TEMP 600 } {$TEMP>=300} {incr TEMP -1} {
reassignTemp $TEMP
run 2000
}
run 1000000
run 8000000
reassignFreq 2000
reassignTemp 0
minimize 2000
for { set TEMP 0 } {$TEMP<601} {incr TEMP 1} {
reassignTemp $TEMP
run 2000
}
run 1000000
for { set TEMP 600 } {$TEMP>=300} {incr TEMP -1} {
reassignTemp $TEMP
run 2000
}
run 1000000
run 8000000
Minimization command doesn't work with langevin piston on,
so I have to switch it off for minimization and then
switch to on to run MD.
When namd analyze the conf file the bottom error is
written out and the program stops.
Someone could help me to solve the problem?
ERROR: Multiple definitions of 'LangevinPiston'
ERROR: in the configuration file are not allowed
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
Thank in advance
Roberta
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