VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Mon Oct 31 2016 - 21:38:12 CDT

I will take a look soon. Please bug me personally if you don’t hear anything within a couple days.

Best,
JC

> On Oct 31, 2016, at 2:15 PM, Eisenhart, Andrew (eisenhaw) <eisenhaw_at_mail.uc.edu> wrote:
>
> Hello,
>
> I am attempting to complete the charge optimization for a fragment of my molecule using VMD-fftk (1.9.2). I am receiving the following error code when running the optimization.
>
>
> measure bond: must specify exactly two atoms in a list
> measure bond: must specify exactly two atoms in a list
> while executing
> "measure bond "[$temp1 get index] [$temp2 get index]" frame $i"
> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 215)
> invoked from within
> "::ForceFieldToolKit::ChargeOpt::optimize"
> (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
> invoked from within
> "::ForceFieldToolKit::gui::coptRunOpt "
> invoked from within
> ".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
> invoked from within
> ".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} { .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed; .fftk_gui.hlf.nb.chargeopt.runOpt in..."
> (command bound to event)
>
> There are few similar questions on the mailing list already, but no solutions that have worked for me. I've tried simulated annealing and downhill with no success.
>
> I can replicate the error when loading as few as one log file.
>
> Here is a link to my box folder that contains my .log and other initial files. https://uc.box.com/s/3vye3uqw8d90vpqyn0qgm08k4s5sgf18 <https://uc.box.com/s/3vye3uqw8d90vpqyn0qgm08k4s5sgf18>
> This folder contains the Gaussian input files i used to generate the log files. https://uc.box.com/s/udepalaygv1sq2xqwwka9ox10vl3mr5j <https://uc.box.com/s/udepalaygv1sq2xqwwka9ox10vl3mr5j>
> <https://uc.box.com/s/ku0ujld45bjirmut8xbelcxlukuhoq42> <https://uc.box.com/s/3vye3uqw8d90vpqyn0qgm08k4s5sgf18>
> Thanks for your time!
>
>
> -Andrew Eisenhart