VMD-L Mailing List

From: Domenico Riolfi Barzotto (domenicobar_at_iq.usp.br)
Date: Fri Dec 18 2020 - 11:22:56 CST

It was generated by avogadro.
Cordially,
Domenico Barzotto

Em sex., 18 de dez. de 2020 às 13:15, John Stone <johns_at_ks.uiuc.edu>
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
> > 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/
>