VMD-L Mailing List

From: Nicolás Veiga (nveiga_at_fq.edu.uy)
Date: Fri Dec 14 2018 - 14:57:59 CST

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