VMD-L Mailing List

From: SEZEN VATANSEVER (svatansever13_at_ku.edu.tr)
Date: Thu Nov 20 2014 - 06:23:43 CST

Dear Christopher Mayne,
Althougtmy new hess LOG file terminateswith"Normal termination of
Gaussian", I got a new error:

"unmatched open quote in list
unmatched open quote in list
    while executing
"lrange $line 0 1"
    (procedure "read_harmonic_frequencies" line 18)
    invoked from within
"read_harmonic_frequencies $file"
    (procedure "::QMtool::load_gaussian_log" line 58)
    invoked from within
"::QMtool::load_gaussian_log $hessLog $hessLogID"
    (procedure "::ForceFieldToolKit::BondAngleOpt::optimize" line 81)
    invoked from within
"::ForceFieldToolKit::BondAngleOpt::optimize"
    (procedure "::ForceFieldToolKit::gui::baoptRunOpt" line 40)
    invoked from within
"::ForceFieldToolKit::gui::baoptRunOpt "
    invoked from within
".fftk_gui.hlf.nb.bondangleopt.runOpt invoke "
    invoked from within
".fftk_gui.hlf.nb.bondangleopt.runOpt instate {pressed !disabled} {
.fftk_gui.hlf.nb.bondangleopt.runOpt state !pressed;
.fftk_gui.hlf.nb.bondangleopt...."
    (command bound to event)"

> Sezen,
>
> It seems that the error is triggered while extracting data from the
> hessian LOG file; this is the first place I would look. Open the hessian
> LOG file and look at the very end for "Normal termination of Gaussian" to
> check if the calculation completed normally. If it did not, then there is
> something wrong with that calculation.
>
> If the hessian calculation did complete normally can you zip up and send
> me the following files?
> initial PSF, geometry optimized PDB, initial parameter (PAR) file,
> from the geometry optimization, the input (GAU), output (LOG), and
> checkpoint (CHK) files
> from the hessian calculation, the input (GAU), output (LOG) files
>
> Regards,
> Christopher Mayne
>
> On Nov 12, 2014, at 6:51 AM, Ashar Malik wrote:
>
> Hey,
>
> You probably need to give a little more detail. From the error it can be
> speculated that you are trying to just MULTIPLY something and one of then
> or maybe both have not been initialized.
>
> You will have to look at this yourself, or provide more detail, if you
> expect some constructive feed back.
>
> Best,
> /A
>
> On Wed, Nov 12, 2014 at 11:40 PM, SEZEN VATANSEVER <
> svatansever13_at_ku.edu.tr> wrote:
>
>> * Dear VMD users/experts, *
>> * I have been trying to use the Force field toolkit in VMD 1.9.2 Beta
>> (Windows) to parameterize a new molecule. **In the "Opt.Bonded" tab,
>> when I tried to Run Optimisation, I got the ** I got the following error
>> message: *
>>
>>
>> * "can't use empty string as operand of "*" can't use empty string as
>> operand of "*" while executing "expr {($kc)*$h1up*$h2up}"
>> (procedure "::ForceFieldToolKit::BondAngleOpt::computePESqm" line 197)
>> invoked from within "::ForceFieldToolKit::BondAngleOpt::computePESqm
>> $hessLogID" (procedure "::ForceFieldToolKit::BondAngleOpt::optimize"
>> line 93) invoked from within
>> "::ForceFieldToolKit::BondAngleOpt::optimize" (procedure
>> "::ForceFieldToolKit::gui::baoptRunOpt" line 40) invoked from within
>> "::ForceFieldToolKit::gui::baoptRunOpt " invoked from within
>> ".fftk_gui.hlf.nb.bondangleopt.runOpt invoke " invoked from within
>> ".fftk_gui.hlf.nb.bondangleopt.runOpt instate {pressed !disabled} {
>> .fftk_gui.hlf.nb.bondangleopt.runOpt state !pressed;
>> .fftk_gui.hlf.nb.bondangleopt...." (command bound to event)" I found a
>> solution offer from there:
>> http://guido.vonrudorff.de/force-field-toolkit-empty-string-during-bonded-optimization/
>> But it didn't help me. Is there any way to solve this problem? *
>>
>>
>
>
> --
> Best,
> /A
>
>
>
>