VMD-L Mailing List
From: Massimiliano Porrini (mozz76_at_gmail.com)
Date: Tue Feb 25 2014 - 16:18:25 CST
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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 spacelist 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 M.porrini_at_ed.ac.uk maxp_at_iesl.forth.gr mozz76_at_gmail.com
- Next message: Mayne, Christopher G: "Re: issue(s) with ffTK of vmd-1.9.2a35"
- Previous message: Michail Palaiokostas Avramidis: "RE: Nanostructure Plugin from TCL Script"
- Next in thread: Mayne, Christopher G: "Re: issue(s) with ffTK of vmd-1.9.2a35"
- Reply: Mayne, Christopher G: "Re: issue(s) with ffTK of vmd-1.9.2a35"
- Reply: Tim Lo: "Re: issue(s) with ffTK of vmd-1.9.2a35"
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