From: Lada Biedermannová (lada.biedermannova_at_img.cas.cz)
Date: Wed Apr 27 2011 - 09:08:46 CDT
Dear all,
I would like to perform the "Free Energy of Conformational Change"
type of calculation in NAMD. Specifically, I need to calculate a free
energy change of applying a harmonic restraint on a certain distance.
The problem is that my topology is in amber format. How can I specify
the segname for my molecule? I have tried both "{}" and "main" as
segname, but I keep getting parsing errors.
Could you please help me solve this problem?
Thanks in advance,
Lada Biedermannova
-----------------
Input:
-----------------
freeEnergy on
freeEnergyConfig {
urestraint {
dist ({}, 295, C) group {({}, 37, ND2), ({}, 108, NE1)} kf=10.0 ref=2.3
}
mcti {
task = stepfade
numsteps = 10
equiltime = 10 ps
accumtime = 100 ps
print = 10 ps
}
}
-----------------
Output:
-----------------
FreeEnergy: Problem parsing input parameters
FreeEnergy: Error: Can't Read Atoms
FreeEnergy: Read Until: ({}, 295, c) group {({}, 37, nd2), ({},
108, ne1)} kf=10.0 ref=2.3
}
mcti {
task = stepfade
numsteps = 10
equiltime = 10 ps
accumtime = 100 ps
print = 10 ps
}
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