VMD-L Mailing List

From: mariano spivak (mariano_at_ks.uiuc.edu)
Date: Tue Sep 10 2019 - 16:05:34 CDT

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

mspivak_at_illinois.edu

On Mon, Sep 9, 2019 at 8:08 PM #YEO JINGJIE# <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> 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
>
> mspivak_at_illinois.edu
>
> On Mon, Sep 9, 2019 at 2:45 AM #YEO JINGJIE# <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.
>