From: Jason Smith (
Date: Fri Dec 18 2020 - 12:37:51 CST

Hi Domenico,

in my experience tools like avogadro and vegazz can be great for somethings and very buggy for other things. The quickest solution is likely to load the pdb and psf that VMD generated prior to the simulation. This should fix a lot of issues. Some programs like old versions of MOE, simply don't generate a PDB that VMD can understand without for e.g. deleting the connect records.

Always be very wary of taking files generated from one program and assuming they will work in another. Some sort of validation should always be done. I've had issue with SMILES that Schroedinger couldn't interpret correctly because Schroedinger expected explicit bonds instead of a Kekule structure. Even the most expensive and heavily developed software can't predict every use case.


Jason Smith
Post-Doctoral Fellow
Robert N. Young Lab, Simon Fraser University
8888 University Drive, Burnaby, BC, V5A-1S6

From: <> on behalf of Domenico Riolfi Barzotto <>
Sent: Friday, 18 December 2020 9:22:56 AM
To: John Stone; Domenico Riolfi Barzotto;
Subject: Re: vmd-l: Molecule is shown with too many bonds

It was generated by avogadro.
Domenico Barzotto

Em sex., 18 de dez. de 2020 ās 13:15, John Stone <<>> escreveu:
What software generated the PDB file that you're loading?

Best regards,
  John Stone

> 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
> 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

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349