VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Nov 17 2014 - 13:43:48 CST

Sezen,

Based on the files you sent me (offline), the Gaussian LOG files do not indicate normal termination status. Strangely, they don't indicate an error status either, the LOG file just stops. it appears that something is killing the job before it finishes. I suggest that you perform some simple test calculations to check your G09 install.

Regards,
Christopher Mayne

On Nov 12, 2014, at 8:04 AM, Mayne, Christopher G wrote:

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<mailto: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