From: vermaasj (vermaasj_at_msu.edu)
Date: Fri Dec 18 2020 - 10:32:43 CST

Hi Domenico,

This is the important line:

Determining bond structure from distance search ...

VMD is guessing bonds using distance based heuristics, which are *usually* pretty good, but sometimes pdb structures have distances that are too short. I donít know what pymol uses, but I suspect they use a different bond determination algorithm. Usually, folks will create a psf file with correct bond structure and load that first, so that VMD does not have to guess bonded structure.

-Josh

From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu>
Date: Friday, December 18, 2020 at 8:22 AM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Molecule is shown with too many bonds
Hello,
I am a newbie to molecular dynamics and computing in general. I've been trying to set up VMD on my laptops (one is Windows 10 and the other Ubuntu 18). On both of them the installation seemed to go fine. But when I try opening my peptide pdb file, it shows a structure with way too many bonds that should not exist, for example the oxygen on the phenol group is shown to be bonded to both of the ortho position carbons. I have tried to install different versions but they all have the same problem. When I open the file on pyMOL it appears fine. Here is what VMD prints on both of my computers when I open the file:

Info) Multithreading available, 4 CPUs detected. Info) Free system memory: 2047MB (100%) Info) OpenGL renderer: Intel(R) HD Graphics 630 Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVFGS) Info) Full GLSL rendering mode is available. Info) Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8) Info) No joysticks found. Joystick interface disabled.
Info) Dynamically loaded 76 plugins in directory: Info) C:/Program Files (x86)/VMD/plugins/WIN32/molfile Info) File loading in progress, please wait. Info) Using plugin pdb for structure file s-QYP.pdb Info) Using plugin pdb for coordinates from file s-QYP.pdb Info) Determining bond structure from distance search ... Info) Eliminating bonds duplicated from existing structure... Info) Finished with coordinate file s-QYP.pdb. Info) Analyzing structure ...
Info) Atoms: 169
Info) Bonds: 339
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0 Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info) Residues: 11
Info) Waters: 0
Info) Segments: 1

Thanks in advance,
Domenico Barzotto