VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Fri Dec 14 2018 - 18:04:17 CST

Unfortunately there’s no way to know for sure what went wrong. Try running something else that uses NAMD, like namdenergy, and see if that works. You could also try calling NAMD from the VMD console using exec, just as done in the command in the error.

Best,
JC

On Dec 14, 2018, at 6:38 PM, Nicolás Veiga <nveiga_at_fq.edu.uy<mailto:nveiga_at_fq.edu.uy>> wrote:

Thanks for the prompt reply!

The only new file in my working directory is “BondedOpt.debug.log”. It seems that everything went well there. The last lines of the file (which is attached to this email) are:

END


NAMD run complete

Apart from that, in the VMD working directory I could find the file “min-bondangles.conf” (which is also attached to this email). There is no .log file in this directory.

Regards,

Nicolás.

Dr. Nicolás Veiga
Profesor Adjunto de Química Inorgánica
Facultad de Química - UdelaR
Montevideo, Uruguay
Contacto: +598 924 97 39

From: Gumbart, JC
Sent: Friday, December 14, 2018 7:51 PM
To: Nicolás Veiga
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: fftk problem in opt. bonded step

It sounds like something is going wrong with NAMD. Can you happen to find that *.namd and *.log file in your directory and see what error is there, if any?

Best,
JC

On Dec 14, 2018, at 3:57 PM, Nicolás Veiga <nveiga_at_fq.edu.uy> wrote:

Hello,

I am trying to parameterize a substrate using the force field toolkit (ffTK) plugin for VMD. Everything went well until I reached the bond and angle optimization step. After the calculation of the Hessian matrix, I uploaded the information with the “Guess” button. However, when I tried to optimize the parameters, I got the following error:

child killed: unknown signal
child killed: unknown signal
    while executing
"exec $namdcmd ${jobname}-temp.namd > ${jobname}-temp.log"
    (procedure "namdrun" line 56)
    invoked from within
"namdrun"
    (procedure "namdmain" line 76)
    invoked from within
"namdmain"
    (procedure "::namdEnergy::namdenergy" line 176)
    invoked from within
"::namdEnergy::namdenergy -silent -psf C:/work/Cu_ala_phe_phen_autopsf_opt.psf -exe C:/NAMD/namd2.exe -all -sel atomselect496430 -cutoff 1000 -par C:/w..."
    ("eval" body line 1)
    invoked from within
"eval ::namdEnergy::namdenergy $args"
    (procedure "namdenergy" line 1)
    invoked from within
"namdenergy -silent -psf C:/work/Cu_ala_phe_phen_autopsf_opt.psf -exe C:/NAMD/namd2.exe -all -sel $sel -cutoff 1000 -par C:/work/Cu_ala_phe_phen_initia..."
    ("eval" body line 1)
    invoked from within
"eval $namdEn"
    (procedure "::ForceFieldToolKit::BondAngleOpt::computePESmm" line 39)
    invoked from within
"::ForceFieldToolKit::BondAngleOpt::computePESmm $moleculeID $baIndList $namdEnCommand"
    (procedure "::ForceFieldToolKit::BondAngleOpt::optBondsAngles" line 84)
    invoked from within
"$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 324)
    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)

I have tried to solve the problem by following the instructions in https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/24850.html and https://guido.vonrudorff.de/2013/force-field-toolkit-empty-string-during-bonded-optimization/. However, I still get the same error message.

Is there a solution for this problem?

Thanks in advance, regards,

Nicolás.

Dr. Nicolás Veiga
Profesor Adjunto de Química Inorgánica
Facultad de Química - UdelaR
Montevideo, Uruguay
Contacto: +598 924 97 39

<BondedOpt.debug.log><min-bondangles.conf>