VMD-L Mailing List

From: Tim Lo (timlo_at_hku.hk)
Date: Tue Feb 25 2014 - 19:38:52 CST

Dear Masimiliano,

I have experienced a similar problem before too. When I loaded the log
files into "Water Int.", my observations were the same as yours.

When I ignored this error and started using "Opt. Charges", the error
that I got was a bit different from yours:/
//can't use empty string as operand of "-"//
//can't use empty string as operand of "-"//
// while executing//
//"expr {[lindex $y 1]-$T*log(rand())}"//
// (procedure "simulated_annealing" line 30)//
// invoked from within//
//"simulated_annealing $T "//
// (procedure "::Optimize::Opt1::handle" line 202)//
// invoked from within//
//"$opt start"//
// (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 421)//
// invoked from within//
//"::ForceFieldToolKit::ChargeOpt::optimize"//
// (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)//
// invoked from within//
//"::ForceFieldToolKit::gui::coptRunOpt "//
// invoked from within//
//".fftk_gui.hlf.nb.chargeopt.runOpt invoke "//
// invoked from within//
//".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} {
.fftk_gui.hlf.nb.chargeopt.runOpt state !pressed;
.fftk_gui.hlf.nb.chargeopt.runOpt in..."//
// (command bound to event)//
/
Then, the TK console said:
/Optimization completed. -- Stationary point found.//
//Optimization completed. -- Stationary point found.//
//No mulliken charges found.//
//Optimization completed. -- Stationary point found.//
//Optimization completed. -- Stationary point found.//
//No mulliken charges found.//
//Creating namespace ::Optimize::Opt0//
//Starting 0-dimensional optimization.//
//Starting optimization with following simplex://
//0: --> 7321.657410393737//
//Simulated annealing://
//Initial temperature T0=25.0//
//Number of T cycles Tsteps=20//
//Simulated annealing step 0: T=25.0//
//Optimization completed. -- Stationary point found.//
//Optimization completed. -- Stationary point found.//
//No mulliken charges found.//
//Optimization completed. -- Stationary point found.//
//Optimization completed. -- Stationary point found.//
//No mulliken charges found.//
//Creating namespace ::Optimize::Opt1//
//Starting 0-dimensional optimization.//
//Starting optimization with following simplex://
//0: --> 7321.657410393737//
//Simulated annealing://
//Initial temperature T0=25.0//
//Number of T cycles Tsteps=20//
//Simulated annealing step 0: T=25.0/

I think this error is due to the different keywords/ keyword order used
in Gaussian09 Rev. D.01, compared to Gaussian09 Rev. C.01. I solved this
problem by using Rev. C.01 to calculate the water interactions. I
suggest using Gaussian09 Rev. C.01 to try it again to check if the same
error appears again.

Regards,
Tim

On 2014/2/26 ?? 06:18, Massimiliano Porrini wrote:
> Dear all,
>
> I am experiencing some problems with the valuable ffTK of VMD version
> 1.9.2a35 .
>
> I could very smoothly reach the step of QM interaction with water
> molecules.
>
> Indeed, I generated the Gaussian input files for the interaction with the
> water molecule, then I ran G09 with them and I successfully obtained
> the related log files.
>
> But, in the TAB named "Water Int.", if I try to upload these log
> files to check the optimised geometry, the following error message
> pops up:
>
>
> /Couldn't read 'Input orientation'!/
>
>
> And in the TkConsole the following lines appear (for each .log file I
> attempted
> to upload):
>
>
> /Reading internal coordinates from 'Initial Parameters'.
> No 'Initial Parameters' section found!
> No cartesian coordinates given in Z-matrix.
> Reading 'Input Orientation'./
>
>
> Besides, in the end, the following message shows up:
>
>
> /list element in quotes followed by "," instead of space
> list element in quotes followed by "," instead of space
> while executing
> "lindex $line 0"
> (procedure "::QMtool::read_gaussian_log" line 154)
> invoked from within
> "::QMtool::read_gaussian_log $logfile $molId"
> ("foreach" body line 5)
> invoked from within
> "foreach logfile $::ForceFieldToolKit::gui::gzmLOGfiles {
> set molId [mol new]
> ::QMtool::use_vmd_molecule $molId..."
> invoked from within
> ".fftk_gui.hlf.nb.genzmat.run.loadLOG invoke "
> invoked from within
> ".fftk_gui.hlf.nb.genzmat.run.loadLOG instate {pressed !disabled} {
> .fftk_gui.hlf.nb.genzmat.run.loadLOG state !pressed;
> .fftk_gui.hlf.nb.genzmat.run.l..."
> (command bound to event)/
>
>
> However, if I try to skip this step (which is supposed to be just a
> visualization check of
> the optimised geometries with water) and I use the G09 log files for
> the Charge Optimisation
> step, I get the following error:
>
>
> /atomselect set: 0 data items doesn't match 1 selected atoms.
> atomselect set: 0 data items doesn't match 1 selected atoms.
> while executing
> "$temp set x [lindex [lindex $molCoords $i] 0]"
> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 187)
> invoked from within
> "::ForceFieldToolKit::ChargeOpt::optimize"
> (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
> invoked from within
> "::ForceFieldToolKit::gui::coptRunOpt "
> invoked from within
> ".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
> invoked from within
> ".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} {
> .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed;
> .fftk_gui.hlf.nb.chargeopt.runOpt in..."
> (command bound to event)/
>
>
> And in the TkConsole:
>
>
> /Error termination request processed by link 9999.
> No mulliken charges found.
> No mulliken charges found.
> Optimization completed. -- Stationary point found.
> Optimization completed. -- Stationary point found.
> ***
> No mulliken charges found.
> Error termination via Lnk1e in
> /r1/software/g09revD01_nehalem/g09/l1.exe at Tue Feb 25 10:25:16 2014./
>
>
> Has anybody already encountered and hopefully got this(these) issue(s)
> sorted out?
>
> Best wishes,
>
>
> PS If necessary, I might also send off list the "debugging log file" I
> obtained from this last step.
>
>
>
> --
> Dr Massimiliano Porrini
> Institut Européen de Chimie et Biologie (IECB)
> CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
> 2, rue Robert Escarpit
> 33607 Pessac Cedex
> France
> http://www.iecb.u-bordeaux.fr/
>
> Emails: m.porrini_at_iecb.u-bordeaux.fr <mailto:m.porrini_at_iecb.u-bordeaux.fr>
> M.porrini_at_ed.ac.uk <mailto:M.porrini_at_ed.ac.uk>
> maxp_at_iesl.forth.gr <mailto:maxp_at_iesl.forth.gr>
> mozz76_at_gmail.com <mailto:mozz76_at_gmail.com>