VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 19 2021 - 15:08:54 CDT

Hi,
  Please try the new VMD 1.9.4a55 test builds for MacOS.
They contain a fix for a bug in psfgen that could hang or crash
in some circumstances. We are aware of a different outstanding problem
with QwikMD and plotting in Tk 8.6.x, and a fix is in development but won't
be available until the next test version.

Best,
  John Stone

On Mon, Oct 18, 2021 at 12:20:17PM -0500, John Stone wrote:
> Hi,
> I will soon be preparing a new VMD build that contains updates to
> psfgen that may resolve this specific issue.
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sat, Oct 02, 2021 at 12:57:21PM +0000, Carolyn Fitch wrote:
> > 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
>
> --
> 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/ 

-- 
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/