Re: Fwd: colvars: keyword "name" is not supported, or not recognized in this context.

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Jan 15 2015 - 10:34:22 CST

Hi Francesco,

I suspect the closing braces at the end of comment lines:
    group1 { atomNumbers 7950 # atom NE2, resid MOL499 }

If the line ends with a comment, put the closing brace on the next line.

Jerome

On 15 January 2015 at 17:10, Francesco Pietra <chiendarret_at_gmail.com> wrote:

> Forgot to mention that I tried to run minimization (VelocityQuenching)
> with an amber .parm7 file.
> fp
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Thu, Jan 15, 2015 at 4:52 PM
> Subject: colvars: keyword "name" is not supported, or not recognized in
> this context.
> To: NAMD <namd-l_at_ks.uiuc.edu>
>
>
> 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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