From: Gumbart, JC (
Date: Tue Feb 23 2021 - 19:28:33 CST

Sorry, I wasn’t clear: I can reproduce the error on my mac, but not in linux, i.e., it works fine in linux. It’s not related to NAMD.


On Feb 23, 2021, at 8:24 PM, Ruijie Darius Teo <<>> wrote:

Hi JC,

Many thanks for the help and hard work! I am very grateful. I currently use a Mac with the 8.6.10 version. It is strange that it works on your Mac but not on mine.

For the NAMD bin, I am currently using NAMD_2.13_MacOSX-x86_64-multicore/namd2. Should I try a different version?

Thanks so much,
From: Gumbart, JC <<>>
Sent: Tuesday, February 23, 2021 6:00 PM
To: Ruijie Darius Teo <<>>
Cc:<> <<>>
Subject: Re: vmd-l: Couldn't read internal coordinate table and list index out of range


Hi Darius,

I spent a couple of hours trying to figure out the source of this using the files you sent me yesterday. I can reproduce it on my Mac but not on Linux using identical VMD versions (a48). Even then, I can’t track down what’s causing it. All I can guess is that it might be related to the TCL version (8.5.6 on Linux and 8.6.10 on Mac).

Do you have access to a Linux machine? That would be the fastest solution.


On Feb 23, 2021, at 2:58 PM, Ruijie Darius Teo <<>> wrote:

To the developers/users of FFTK,

I have been using FFTK and have no problems with optimizing charges and dihedrals for my molecule. However, in the Opt. Bond and Angle section, I have encountered an error when hitting the "Guess" or "Run Optimization" box, after providing the necessary psf ,pdb, par, and hess files.

The error first says "Couldn't read internal coordinate table," followed by,

list index out of rangelist index out of range while executing"lset zmatIn 0 6 1" (procedure "assign_fc_zmat" line 36) invoked from within"assign_fc_zmat $targetklist $molid $zmatqm $BAonly" (procedure "::ForceFieldToolKit::BondAngleOpt::computePESqm" line 225) invoked from within"::ForceFieldToolKit::BondAngleOpt::computePESqm $hessLogID" (procedure "::ForceFieldToolKit::BondAngleOpt::optimize" line 93) 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 wondering if you might know what the problem is. I have checked that the atom names and numbers are consistent.

If it helps, here are the settings used for my hessian calculation,

# MP2/6-31G* Geom=(AllCheck,ModRedundant) Freq NoSymm IOp(7/33=1) SCF=Tight Guess=Read

Thanks so much,