VMD-L Mailing List

From: utku.ozkan_at_bilkent.edu.tr
Date: Wed Nov 09 2022 - 00:05:50 CST

Hello,

I am currently trying to create angles for a system using guess angles
tcl script from topotools. The bonds that will be used to guess the
angles are present in my data file. The topo readlammpsdata script
produces the following output as expected:

Info) readlammpsdata: detected triclinic cell.
Info) parsing LAMMPS Masses section.
Info) parsing LAMMPS Atoms section with style ‘full’.
Info) applying atoms data. sorted by atom id.
Info) parsing LAMMPS Bonds section.
Info) applying bonds data.
Info) Analyzing structure …
Info) Atoms: 2700
Info) Bonds: 5400
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 1 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 1
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 0 Nucleic: 0

However the “topo guessangles” function does not produce the angles from
the bond data. “topo getbondlist” successfully returns the defined bond
list. I have read, but could not understand the function algorithm “proc
::TopoTools::guessangles {sel}” provided in “topotools/topoangles.tcl at
865e1ff3c9995ddb7d0f6b66c301303c2c6890c5 · akohlmey/topotools · GitHub”.

Is it possible that the “guessangles” function utilizes the van der
Waals radiuses of the atoms to guess the angles? As my structure has
unusual(long) bonds which “guessbonds” function, previously, could not
assign based on atom coordinates and types.