From: Eisenhart, Andrew (eisenhaw) (
Date: Mon Nov 07 2016 - 13:33:39 CST

Ahh I see, that seems to have solved the problem. Thanks for all of your help everyone!


From: JC Gumbart <>
Sent: Saturday, November 05, 2016 7:30:33 PM
To: Eisenhart, Andrew (eisenhaw)
Cc: Christopher G Mayne;
Subject: Re: vmd-l: FFTK measure bond error

The problem is your resname of 00 (zero zero). This screws up the atomselection. It can be handled by putting it in quotes ( \Ē00\Ē), but will likely cause trouble throughout FFTK and other plugins. The easiest solution is to give it a different name in your input PSF and PDB.


On Nov 2, 2016, at 12:27 PM, Eisenhart, Andrew (eisenhaw) <<>> wrote:

Just checked again and the taget data section does parse the individual O15 files correctly. I even get the same error when using just one of the O15 files so I think the problem is more general. The also the pdb and the psf files are on the second page of the chargeOpt folder.

From: JC Gumbart <<>>
Sent: Tuesday, November 01, 2016 3:39:40 PM
To: Christopher G Mayne
Cc: Eisenhart, Andrew (eisenhaw);<>
Subject: Re: vmd-l: FFTK measure bond error

Oh yeah, check these things first. If youíre still stuck, let us know.

Thanks Chris!

On Nov 1, 2016, at 11:45 AM, Mayne, Christopher G <<>> wrote:


Iím going to need the PSF and geometry optimized PDB file in order to try to reproduce your error. However, I already have one suspicion: when you load in the Gaussian target data, the parser attempts to assign the atom name based on the file name. In older versions of ffTK (Iím pretty sure that I changed this), when scanning multiple angles for carbonyls, the parsed atom name is e.g., O15-120a rather than O15. Make sure that you double check the atom name assignment in the QM Target Data section.

Christopher Mayne

On Oct 31, 2016, at 9:38 PM, JC Gumbart <<>> wrote:

I will take a look soon. Please bug me personally if you donít hear anything within a couple days.


On Oct 31, 2016, at 2:15 PM, Eisenhart, Andrew (eisenhaw) <<>> wrote:


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
    (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.>
This folder contains the Gaussian input files i used to generate the log files.>
Thanks for your time!

-Andrew Eisenhart