VMD-L Mailing List

From: Norfarisha Mohd Fadil (farishafadil_at_live.com)
Date: Wed Jun 07 2017 - 20:04:51 CDT

Hello. I tried opening GROMACS file using the command "vmd umbrella0.gro umbrella0.trr" and it wouldn't open. Below are the notes generated in the terminal:

biotech_at_biotechutm:~/umbrella$ vmd umbrella0.gro umbrella0.trr
/usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 4 CPUs detected.
Info) CPU features: SSE2 AVX AVX2 FMA
Info) Free system memory: 14GB (89%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option. Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
Info) OpenGL renderer: Mesa DRI Intel(R) Kabylake GT2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (8192x8192), 3-D (512x512x512), Multitexture (8)
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
Info) File loading in progress, please wait.
Info) Using plugin gro for structure file umbrella0.gro
Info) Using plugin gro for coordinates from file umbrella0.gro
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file umbrella0.gro.
Info) Analyzing structure ...
Info) Atoms: 33207
Info) Bonds: 22485
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 10862
Info) Waters: 10675
Warning) Unusual bond between residues: 1 (none) and 2 (protein)
Warning) Unusual bond between residues: 28 (none) and 29 (protein)
Warning) Unusual bond between residues: 55 (none) and 56 (protein)
Warning) Unusual bond between residues: 82 (none) and 83 (protein)
Warning) Unusual bond between residues: 109 (none) and 110 (protein)
Info) Segments: 1
Info) Fragments: 10732 Protein: 5 Nucleic: 0
Info) Using plugin trr for coordinates from file umbrella0.trr
Segmentation fault (core dumped)

Can someone help me with this? What might be the issue?

With thanks and regards,

Norfarisha binti Mohd Fadil

Student

Department of Chemistry
Faculty of Science
UTM, Johor Bahru
Malaysia

Phone: +6011-26651278