From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Jan 15 2015 - 09:52:16 CST
Hello:
With nam2.10 on debian amd64 I tried vainly to fix the error in reading a
distance colvars file "keyword "name" is not supported, or not recognized
in this context". I came across a similar questio to namd but it was
connected to the use of microsoft. I have none, anyway I checked for the
absence of carriage returns. The whole file is parted below.
thanks for advice
francesco pietra
# collective variables config file for distances
colvarsTrajFrequency 100
colvarsRestartFrequency 200
colvar {
name c1
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7893 # atom O2 resid MOL499 }
group2 { atomNumbers 1628 # atom CA resid BKB103 }
}
}
colvar {
name c2
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7902 # atom O5 resid MOL499 }
group2 { atomNumbers 2059 # atom CA resid BKB133 }
}
}
colvar {
name c3
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7911 # atom C9 resid MOL499 }
group2 { atomNumbers 2108 # atom CA resid BKB136 }
}
}
colvar {
name c4
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7922 # atom C14 resid MOL499 }
group2 { atomNumbers 3077 # atom CA resid BKB196 }
}
}
colvar {
name c5
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7931 # atom C18 resid MOL499 }
group2 { atomNumbers 3548 # atom CA resid BKB230 }
}
}
colvar {
name c6
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7940 # atom CB resid MOL499 }
group2 { atomNumbers 3589 # atom CA resid BKB233 }
}
}
colvar {
name c7
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7956 # atom C resid MOL499 }
group2 { atomNumbers 7937 # atom CD resid MOL }
}
}
colvar {
name c8
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7937 # atom CD resid MOL499 }
group2 { atomNumbers 7908 # atom C8 resid MOL }
}
}
colvar {
name c9
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7955 # atom FE resid MOL499 }
group2 { atomNumbers 7951 # atom FE1 resid MOL }
}
}
colvar {
name c10
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7901 # atom O2, resid MOL499 }
group2 { atomNumbers 7915 # atom N1, resid MOL }
}
}
colvar {
name c11
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7901 # atom O2, resid MOL499 }
group2 { atomNumbers 7952 # atom O7, resid MOL }
}
}
colvar {
name c12
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7962 # atom OXT, resid MOL499 }
group2 { atomNumbers 7930 # atom O6, resid MOL }
}
}
colvar {
name c13
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7930 # atom O6, resid MOL499 }
group2 { atomNumbers 7950 # atom NE2, resid MOL }
}
}
colvar {
name c14
width 0.2
lowerBoundary -10.0
upperBoundary 10.0
lowerWall -5.0
upperWall 5.0
lowerWallConstant 100.0
upperWallconstant 100.0
distance {
group1 { atomNumbers 7950 # atom NE2, resid MOL499 }
group2 { atomNumbers 7910 # atom O4, resid MOL }
}
}
harmonic1 {
colvars c1 c2 c3 c4 c5 c6 c7 c8 c9 c10 c11 c12 c13 c14
centers 1.53 1.53 1.53 1.53 1.53 1.53 3.71 3.95 3.90 3.03 3.02 3.00 3.17
3.04
forceConstant 10.0
}
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