VMD-L Mailing List

From: #YEO JINGJIE# (JYEO1_at_e.ntu.edu.sg)
Date: Wed Sep 18 2019 - 20:23:54 CDT

Hi Mariano,

Thank you so much for the prompt response and I'm looking forward to the new build!

Best,
JJ

On 18 Sep 2019, at 12:01 AM, mariano spivak <mariano_at_ks.uiuc.edu<mailto:mariano_at_ks.uiuc.edu>> wrote:

Hi again,

Thanks for letting me know of the problem. I found a bug in the code that was exposed by your calculations and fixed it.
John Stone will be releasing a new build of VMD with this fix later this week.

Let us know if you have any other issues.

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 Tue, Sep 10, 2019 at 4:05 PM mariano spivak <mariano_at_ks.uiuc.edu<mailto:mariano_at_ks.uiuc.edu>> wrote:
Hi,

If you are willing to share the files with me, I can try to figure out the problem and apply a fix if needed.

Thanks

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 8:08 PM #YEO JINGJIE# <JYEO1_at_e.ntu.edu.sg<mailto:JYEO1_at_e.ntu.edu.sg>> wrote:
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.

**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.