VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Sun Dec 16 2018 - 12:53:17 CST

I concur with JC that this is most likely an error that is occurring with NAMD. The error traces back to the namdenergy call, specifically; however, the traceback doesn’t give us enough information to debug the problem directly.

Recreating the actual call isn’t obvious from the traceback, so I dug back into the code.

Load the charge-optimized PSF
Add the geometry-optimized PDB

set sel [atomselect top all]

namdEnergy::namdenergy -psf <path_to_psf> -exe C:/NAMD/namd2.exe -all -sel $sel -cutoff 1000 -par <path_to_parameters>

Note: that a separate “-par <path_to_parameters>” will need to be added for every required parameter file, including the in-progress files, i.e., -par parfile1.prm -par parfile2.prm …

Regards,
Chris

> On Dec 14, 2018, at 4:04 PM, Gumbart, JC <gumbart_at_physics.gatech.edu> wrote:
>
> 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 <https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/24850.html> andhttps://guido.vonrudorff.de/2013/force-field-toolkit-empty-string-during-bonded-optimization/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__guido.vonrudorff.de_2013_force-2Dfield-2Dtoolkit-2Dempty-2Dstring-2Dduring-2Dbonded-2Doptimization_&d=DwMGaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=JBqQLS7jZ5whrB0hXJY8MNYcfDrh8UhlGJ2ANxoi8s0&m=Mblz2a9PcdFhxI8Na3DESM3xrrwqHupWuf_YM9Jaju4&s=0Sy-jFPNTv7k6igibn5GBpJIwd-TNonN2LXqXv3OPyI&e=>. 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>
>


  • application/pkcs7-signature attachment: smime.p7s