VMD-L Mailing List

From: #YEO JINGJIE# (JYEO1_at_e.ntu.edu.sg)
Date: Mon Sep 09 2019 - 20:08:27 CDT

Hi Mariano,

Thank you very much for the prompt response. Yes I've already done that actually, I noticed the renaming problem as well, but after renaming the file is where I get the errors.

Best,
JJ

On 10 Sep 2019, at 2:34 AM, mariano spivak <mariano_at_ks.uiuc.edu<mailto:mariano_at_ks.uiuc.edu>> wrote:

Hi,

Thanks for reporting this issue. Please try the following solution and let me know if it works.
On the directory you are working on, if your Hess Output File is *.out check you have a file *_job2_internal.hess
If you have that file, rename it to *_internal.hess and try Run Optimization again.

Best Regards

Mariano Spivak, Ph.D.
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois.
mariano_at_ks.uiuc.edu<mailto:mariano_at_ks.uiuc.edu>
mspivak_at_illinois.edu<mailto:mspivak_at_illinois.edu>

On Mon, Sep 9, 2019 at 2:45 AM #YEO JINGJIE# <JYEO1_at_e.ntu.edu.sg<mailto:JYEO1_at_e.ntu.edu.sg>> wrote:
Dear VMD and FFTK developers,

I was very excited to test out FFTK's capabilities with ORCA 4.2.0 and NAMD 2.13, however I encountered some errors which I couldn't resolve. I've successfully used previous versions of FFTK with Gaussian, so I had some experience with FFTK.

Firstly, when trying to optimise the bonds and angles, after loading the necessary inputs and pressing "Guess", I get the following message:
Reading internal coordinates from 'Initial Parameters'.
No 'Initial Parameters' section found!
No cartesian coordinates given in Z-matrix.
Reading 'Input Orientation'.

I couldn't pin down where exactly this "Initial Parameters" section was supposed to be. In any case, once I press the "Run Optimization" button, I get the next error:
can't use empty string as operand of "-"
can't use empty string as operand of "-"
    while executing
"expr { $baCurVal-[lindex $entry 2 1] }"
    (procedure "::ForceFieldToolKit::BondAngleOpt::optBondsAngles" line 102)
    invoked from within
"$function $p0list"
    (procedure "construct_initial_simplex" line 22)
    invoked from within
"construct_initial_simplex [lindex $args 0] $scale"
    (procedure "::Optimize::Opt0::handle" line 91)
    invoked from within
"$opt initsimplex $baInitial $scale"
    (procedure "::ForceFieldToolKit::BondAngleOpt::optimize" line 322)
    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)

Please let me know how I can debug this issue, thank you!

Best Regards,
JJ

**Disclaimer** The sender of this email does not represent Nanyang Technological University and this email does not express the views or opinions of the University.

**Disclaimer** The sender of this email does not represent Nanyang Technological University and this email does not express the views or opinions of the University.