From: McGuire, Kelly (
Date: Wed Mar 27 2019 - 23:57:34 CDT

I am running into an error in the water interaction FFTK step. I have atom type that is not in the CGENFF parameters, it is copper. I have defined my own parameters based on copper CHARMM parameters from literature. FFTK identifies my copper atom as an Acceptor atom, but can't write a Gaussian Input File for it. The Gaussian Input File, CAI-ACC-Cu.gau, is blank. It correctly writes Gaussian Input Files for my other Acceptor and Donor atoms without problems. What is the workaround at this FFTK step for new atoms that need to be Acceptor atoms? I am using VMD 1.9.4a12. I believe the error is talking about the copper atom. The error says:

atomselect: cannot parse selection text: index
atomselect: cannot parse selection text: index
    while executing
"atomselect top "index $bInd""
    (procedure "::ForceFieldToolKit::GenZMatrix::writeZmat" line 167)
    invoked from within
"::ForceFieldToolKit::GenZMatrix::writeZmat $acceptorAtom acceptor $Gnames $outfile"
    (procedure "::ForceFieldToolKit::GenZMatrix::genZmatrix" line 89)
    invoked from within
    invoked from within
" invoke "
    invoked from within
" instate {pressed !disabled} { state !pressed;"
    (command bound to event)

Kelly L. McGuire

PhD Candidate


Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602