From: Domenico Riolfi Barzotto (
Date: Fri Dec 18 2020 - 08:32:48 CST

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
      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
              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