VMD-L Mailing List
From: Domenico Riolfi Barzotto (domenicobar_at_iq.usp.br)
Date: Fri Dec 18 2020 - 08:32:48 CST
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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
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