VMD-L Mailing List

From: Carolyn Fitch (fitch_at_jhu.edu)
Date: Sat Oct 02 2021 - 07:57:21 CDT

I have attempted to run 1ubq Quikmd test case on a new OS (BigSur) and binary installs.

"Prepare" crashes with a seg fault:
zsh: segmentation fault /Applications/VMD1p9p4a51x8664Rev9.app/Contents/vmd/vmd_MACOSXX86_64

I have appended the terminal output below.

Any thoughts to get this to complete?

Thanks,
Carolyn

Below is complete terminal output:

cfitch1_at_BPH-CF-MB15P ~ % /Applications/VMD1p9p4a51x8664Rev9.app/Contents/vmd/vmd_MACOSXX86_64
Info) VMD for MACOSXX86_64, version 1.9.4a51 (December 21, 2020)
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, 8 CPUs detected.
Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 HT
Info) High-DPI OpenGL display support enabled.
Info) OpenGL renderer: AMD Radeon Pro 460 OpenGL Engine
Info) Features: STENCIL MDE MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (16384x16384x16384), Multitexture (8)
vmd > psfgen) clearing structure, topology, and aliases
psfgen) clearing structure, topology, and aliases
  The PDB is supported by RCSB, the NSF, US PHS, NIH, NCRP, NIGMS, NLM,
and US DoE, who are not liable for the data. PDB files shall not be
sold. See https://urldefense.com/v3/__ftp://ftp.rcsb.org/advisory.doc__;!!DZ3fjg!qcp-N9lzp3mhSdgJgb3fgGnPnlhrVX_QQY-hCQlYQ81DWnNpqNWKdEC9OGrJU7udqA$ for full details.
Info) Using plugin webpdb for structure file 1ubq
Info) Using plugin webpdb for coordinates from file 1ubq
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file 1ubq.
Info) Analyzing structure ...
Info) Atoms: 660
Info) Bonds: 608
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 134
Info) Waters: 58
Info) Segments: 1
Info) Fragments: 59 Protein: 1 Nucleic: 0
2021-10-01 21:32:59.612 vmd_MACOSXX86_64[12935:1229850] Warning: Expected min height of view: (<NSButton: 0x7fb74cd97660>) to be less than or equal to 30 but got a height of 32.000000. This error will be logged once per view in violation.
2021-10-01 21:33:00.736 vmd_MACOSXX86_64[12935:1229850] Warning: Expected min height of view: (<NSButton: 0x7fb74eedb6f0>) to be less than or equal to 30 but got a height of 32.000000. This error will be logged once per view in violation.
Info) In any publication of scientific results based in part or
Info) completely on the use of the program STRIDE, please reference:
Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
Info) assignment. Proteins: structure, function and genetics, 23, 566-579.
Info) Opened coordinate file /var/folders/v4/7kg21jtn1p7djqznnjksfjh80000gq/T/torplot_temp.pdb for writing.
Info) Finished with coordinate file /var/folders/v4/7kg21jtn1p7djqznnjksfjh80000gq/T/torplot_temp.pdb.
Info) Using plugin pdb for structure file /var/folders/v4/7kg21jtn1p7djqznnjksfjh80000gq/T/torplot_temp.pdb
Info) Using plugin pdb for coordinates from file /var/folders/v4/7kg21jtn1p7djqznnjksfjh80000gq/T/torplot_temp.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 76
Info) Bonds: 0
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 76
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 76 Protein: 0 Nucleic: 0
dxplugin) Error reading line.
Info) Analyzing Volume...
Info) Grid size: 180x180x2 (0 MB)
Info) Total voxels: 64800
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=rama-general.dx : DX map
dxplugin) Error reading line.
Info) Analyzing Volume...
Info) Grid size: 180x180x2 (0 MB)
Info) Total voxels: 64800
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=rama-gly.dx : DX map
dxplugin) Error reading line.
Info) Analyzing Volume...
Info) Grid size: 180x180x2 (0 MB)
Info) Total voxels: 64800
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=rama-ileval.dx : DX map
dxplugin) Error reading line.
Info) Analyzing Volume...
Info) Grid size: 180x180x2 (0 MB)
Info) Total voxels: 64800
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=rama-prepro-noGP.dx : DX map
dxplugin) Error reading line.
Info) Analyzing Volume...
Info) Grid size: 180x180x2 (0 MB)
Info) Total voxels: 64800
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=rama-transpro.dx : DX map
dxplugin) Error reading line.
Info) Analyzing Volume...
Info) Grid size: 180x180x2 (0 MB)
Info) Total voxels: 64800
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=rama-cispro.dx : DX map
Info) Analyzing Volume...
Info) Grid size: 36x36x2 (0 MB)
Info) Total voxels: 2592
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=NGLB_FUC.dx : DX map
Info) Analyzing Volume...
Info) Grid size: 36x36x2 (0 MB)
Info) Total voxels: 2592
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=NGLB_no_FUC.dx : DX map
Info) Analyzing Volume...
Info) Grid size: 36x36x2 (0 MB)
Info) Total voxels: 2592
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=MAN_13_AMAN.dx : DX map
Info) Analyzing Volume...
Info) Grid size: 36x36x36 (0 MB)
Info) Total voxels: 46656
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=AMAN_16_AMAN.dx : DX map
Info) Analyzing Volume...
Info) Grid size: 36x36x36 (0 MB)
Info) Total voxels: 46656
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=BMAN_16_AMAN.dx : DX map
Info) Analyzing Volume...
Info) Grid size: 36x36x2 (0 MB)
Info) Total voxels: 2592
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=BGLN_or_AMAN_14_BGLN.dx : DX map
Info) Analyzing Volume...
Info) Grid size: 36x36x36 (0 MB)
Info) Total voxels: 46656
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=BGLN_16_AFUC.dx : DX map
Info) Analyzing Volume...
Info) Grid size: 36x36x2 (0 MB)
Info) Total voxels: 2592
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=BGLN_14_BMAN.dx : DX map
Info) Analyzing Volume...
Info) Grid size: 36x36x2 (0 MB)
Info) Total voxels: 2592
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=AMAN_12_AMAN.dx : DX map
Info) Analyzing Volume...
Info) Grid size: 36x36x2 (0 MB)
Info) Total voxels: 2592
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=AMAN_12_BGLN.dx : DX map
Info) Analyzing Volume...
Info) Grid size: 36x36x2 (0 MB)
Info) Total voxels: 2592
Info) Min: 0 Max: 1 Range: 1
Info) Computing volume gradient map (0 MB)
Info) Added volume data, name=AMAN_14_BGLN.dx : DX map
Starting............ Done!
Info) Opened coordinate file 1ubq_sel.pdb for writing.
Info) Finished with coordinate file 1ubq_sel.pdb.
Info) Using plugin pdb for structure file 1ubq_sel.pdb
Info) Using plugin pdb for coordinates from file 1ubq_sel.pdb
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file 1ubq_sel.pdb.
Info) Analyzing structure ...
Info) Atoms: 602
Info) Bonds: 608
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 76
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0
Welcome to AUTOPSF!
The automatic structure builder.
psfgen) preserving case of names on input
WORKING ON: 2
Info) ======================
Info) Please cite TopoTools as:
Info) Axel Kohlmeyer & Josh Vermaas, (2019). TopoTools: Release 1.8
Info) https://urldefense.com/v3/__https://doi.org/10.5281/zenodo.598373__;!!DZ3fjg!qcp-N9lzp3mhSdgJgb3fgGnPnlhrVX_QQY-hCQlYQ81DWnNpqNWKdEC9OGo8j9TrQg$
Info) ======================

Info) Analyzing structure ...
Info) Atoms: 602
Info) Bonds: 608
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 1 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 76
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0
Info) Opened coordinate file T3_preformat_protein.pdb for writing.
Info) Finished with coordinate file T3_preformat_protein.pdb.
Info) Opened coordinate file T3_preformat_glycan.pdb for writing.
Info) Finished with coordinate file T3_preformat_glycan.pdb.
Info) Opened coordinate file T3_preformat_other.pdb for writing.
Info) Finished with coordinate file T3_preformat_other.pdb.
Info) Opened coordinate file T3_preformat_ion.pdb for writing.
Info) Finished with coordinate file T3_preformat_ion.pdb.
Info) Opened coordinate file T3_preformat_water.pdb for writing.
Info) Finished with coordinate file T3_preformat_water.pdb.

Step 3 done
Info) Using plugin pdb for structure file T3_formatted.pdb
Info) Using plugin pdb for coordinates from file T3_formatted.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 602
Info) Bonds: 608
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 76
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0
pfrag: false ofrag: false allfrag: true osel: qwikmd_protein or qwikmd_nucleic or qwikmd_glycan or qwikmd_lipid nfrag: false
Info) Opened coordinate file T3_formatted_autopsf-temp.pdb for writing.
Info) Finished with coordinate file T3_formatted_autopsf-temp.pdb.
Reading PDB CONECT records...
Info) Opened coordinate file T3_formatted_autopsf-temp.xbgf for writing.
Info) Finished with coordinate file T3_formatted_autopsf-temp.xbgf.
top_all36_prot.rtf top_all36_lipid.rtf top_all36_na.rtf top_all36_carb.rtf top_all36_cgenff.rtf toppar_all36_carb_glycopeptide.str toppar_water_ions_namd.str
DETECTED CHARMM36 NA
zsh: segmentation fault /Applications/VMD1p9p4a51x8664Rev9.app/Contents/vmd/vmd_MACOSXX86_64