VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 16 2020 - 23:31:47 CDT

Hi,
  Please try VMD 1.9.4 alpha 43, which is posted on the web site
for download. This new test build contains a fix which should cure
the behavior you are encountering with FFTK.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 17, 2020 at 12:15:36AM -0400, Mintare Cesiunaite wrote:
> Dear VMD writers,
>
> I am using VMD extension Force Field Toolkit to train on Ethanol. Presently
> I am stuck at the step of Bond&Angle optimization. This particular step
> required NAMD2 installed to run in the background for the calculations.
> This is what I did:
> 1) I downloaded zip file of NAMD_2.13 and extracted it into directory on
> Desktop (since it is said Namd2 can be unzipped and can be run directly)
> 2) I opened Tk Console and led it to the NAMD_2.13 directory on the desktop
> (.....cd Desktop -> cd NAMD_2.13)
> 3) I uploaded the input files (psf, pdb, hess.log, par) in the input
> section and I selected namd2.exe that is in the NAMD_2.13 directory on my
> Desktop
>
> When I run optimization, I get "Child killed: unknown signal" error.
> I have tried placing namd2.exe in different locations as Program files, but
> still get the same error.
>
> I suspect there is miscommunication between the VMD and NAMD2.
>
>
> This is the Details of the error:
>
> child killed: unknown signal
> child killed: unknown signal
> while executing
> "::exec {C:/Program Files/NAMD_2.13_Win64-multicore/namd2.exe}
> min-bondangles.conf"
> ("eval" body line 1)
> invoked from within
> "eval ::exec [list $exec_path] [lrange $args 1 end]"
> (procedure "::ExecTool::exec" line 14)
> invoked from within
> "::ExecTool::exec $namdbin $minName.conf"
> (procedure "::ForceFieldToolKit::BondAngleOpt::optBondsAngles" line 68)
> invoked from within
> "$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 am not sure how to solve it or how to "install NAMD2 correctly. I use
> Windows 10.
>
> Thank you for your assistance.
>
> Sincerely,
> Mintare Cesiunaite
> Student in IUPUI 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/