From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Wed May 04 2011 - 00:55:40 CDT
Dear NAMD Experts,
I am trying to find out the potentials of mean force with respect to the helicity fraction of a portion of the protein through ABF. The colvar config file is listed below -
#Global options:
colvarsTrajFrequency 100
colvarsRestartFrequency 2
analysis off
###########################
colvar {
############################################
name hlx_frac
width 1.0
lower boundary 0.0
upper boundary 1.0
outputValue on
outputVelocity off
outputSystemForce off
outputAppliedForce off
extendedLagrangian off
alpha {
residueRange 71-82
psfSegID ASYN
hBondCoeff 0.5
angleRef 88
angleTol 15
hBondCutoff 3.3
hBondExpNumer 6
hBondExpDenom 8
atomsFile hlx_frac.pdb
atomsCol O
atomsColValue 2.0
}
}
#############################################
# Bias type
abf {
colvars hlx_frac
fullSamples 100
hideJacobian no
outputFreq 100
applyBias yes
}
######################################
The error message which is coming in the output file is -
colvars: Error: cannot add atoms to a dummy group.
colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
Any kind of suggestion or correction will be highly appreciated.
Thanks and regards
Prathit Chatterjee
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