VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 18 2020 - 10:15:13 CST

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
> 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 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/