From: 李耀 (liyao17_at_mails.tsinghua.edu.cn)
Date: Wed Nov 21 2018 - 09:44:53 CST
Dear NAMD users,
I'm trying to run umbrella sampling with amber topology and coordinates files, and this is my conf file:
# input
amber yes
parmfile ../../new_mono.prmtop
ambercoor 0_1.rst
#output
outputname win1
temperature 300 #tempi=300
restartfreq 100
DCDfreq 50
xstFreq 50
outputenergies 50
outputPressure 50
## interpret amber parameters to namd
numsteps 100 #nstlim=100
cutoff 10 #cut=10
switching off
rigidBonds all #ntc=2, ntf=2
rigidTolerance 0.00001 #for amber,tol=0.00001, 0.00000001 for charmm
useSettle on #jfastw=0, default
rigidIterations 100
timestep 2 #dt=0.002
PME on #ntb=1
PMETolerance 0.00001 #dsum_tol=1.0e-5, default
PMEInterpOrder 4 #order=4
PMEGridSpacing 1.0
PMEGridSizeX 90
PMEGridSizeY 90
PMEGridSizeZ 110
cellBasisVector1 78.0575541 0.0 0.0
cellBasisVector2 0.0 61.8352441 0.0
cellBasisVector3 0.0 0.0 103.1854372
cellOrigin 0.0 0.0 0.0
wrapWater on
wrapAll on
#constant pressure control is off
langevinPiston off
BerendsenPressure off #ntp=0
exclude scaled1-4 #default
1-4scaling 1.0
scnb 2.0 #define in prmtop
readexclusions yes
watermodel tip3 #default
pairListDist 11 #skinnb=2, default
LJcorrection on #vdwmeth=1, default
ZeroMomentum on #netfrc=1, default, 0 for minimization
fullElectFrequency 1
nonBondedFreq 1
stepspercycle 10
#temperature control
langevin on #ntt=3
langevinDamping 2 #gamma_ln=2
langevinTemp 300 #temp0=300
langevinHydrogen off
##extra parameters
constraints on
consexp 2 #harmonic constraints(square)
consref oref1.pdb
conskfile oref1.pdb
conscol O
constraintScaling 1.0
colvars on
colvarsConfig win1test2cv.in
#execution script
run 100
But it came out the following error in the log file:
ERROR: 'conskcol' is a required configuration option
ERROR: when 'constraints' is set
ERROR: conskcol defines: Column of conskfile to use for the force constants
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: conscol
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
I'm not familiar with NAMD, so could someone help me to figure out what happened? By the way, I set the occupancy of CA to 1.00, the rest 0.00. Thank you!
Best,
Yao Li
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