VMD-L Mailing List

From: Ronit Sarangi (ronits.chem95_at_gmail.com)
Date: Mon Dec 02 2024 - 12:21:57 CST

Hello,

I want to extract internal coordinates and their values for a system using
QMtool's "modredundant_zmat" function. I know one way to do it via the
Gaussian input file method, e.g.

::QMtool::load_file <path to Gaussian file>
set internals [::QMtool::modredundant_zmat]

But I'm not sure how to do it without the Gaussian input file, i.e., with
just an xyz file,

mol new <xyz_file>
set internals [::QMtool::modredundant_zmat]

gives me the error " Cannot find molecule -1 in atomselect's 'molId' ".
Please let me know if it is possible to use an xyz (or psf and pdb) file
for that.

Best,
Ronit