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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Jan 15 2015 - 10:54:47 CST

Hi Jerome:
That was the case.

There was another mistake: 'hermonic1' should be written 'harmonic',
otherwise not recognized.

Thanks a lot
francesco

PS: you missed to indicate (on my request) which file to edit on new vmd
in order to fix the rlwrap issue (or my request was so pedestrian not to
merit an answer, which is very likely the case)

On Thu, Jan 15, 2015 at 5:34 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> 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
>> }
>>
>>
>>
>>
>

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:33 CST