Error during Opt. Charges while using FF Took Kit

From: Aaron Larsen (
Date: Wed May 20 2015 - 16:38:19 CDT

Hello namd users,

I'm current parameterizing some nucleobase-like molecules and 9/10 are
working just fine. The tenth is giving an error that I am unable to resolve
during the Opt. Charges step. Everything else up to this stage as worked

I found a past instance of this error being discussed on this forum, but
the proposed solution is irrelevant to my problem (the solution was to
solve the water charges using Gaussian, but I've been doing this from the

The error log is as follows:

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)

I'm unable to determine what might be causing this error. The structure is
unremarkable compared to the others that have worked.

Any advice would be appreciated.


Aaron Larsen, Ph.D.
Harvard University Department of Chemistry and Chemical Biology
Harvard Medical School Department of Genetics
Mobile: 617-319-3782
FAX: 617-643-3328

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