VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 19 2021 - 16:55:04 CDT

Mike,
  Thanks for the followup, I'm glad the new build has cured the problem.

We have more updates coming, but I'm happy to hear that we've resolved
the particular problems that had affected structure preparation with psfgen.

Best,
  John Stone

On Tue, Oct 19, 2021 at 09:46:13PM +0000, Mike McCallum wrote:
> This build seems to have fixed the issues we were having.
> Thanks again, John!
> MIke
>
> On Oct 19, 2021, at 1:08 PM, John Stone <[1]johns_at_ks.uiuc.edu> wrote:
> CAUTION: This email originated from outside of Pacific. Do not click any
> links or open attachments if this is unsolicited email.
>
> 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
> [2]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) [3]http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to [4]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
> [5]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)
> [6]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
> [7]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [8]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
> [9]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [10]http://www.ks.uiuc.edu/Research/vmd/
>
> --
> C. Michael McCallum
> Professor
> Department of Chemistry, UOP
> mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209)
> 946-2607 fax
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/Research/vmd/
> 4. mailto:vmd_at_ks.uiuc.edu
> 5. https://urldefense.com/v3/__ftp://ftp.rcsb.org/advisory.doc__;!!DZ3fjg!qcp-N9lzp3mhSdgJgb3fgGnPnlhrVX_QQY-hCQlYQ81DWnNpqNWKdEC9OGrJU7udqA$
> 6. https://urldefense.com/v3/__https://doi.org/10.5281/zenodo.598373__;!!DZ3fjg!qcp-N9lzp3mhSdgJgb3fgGnPnlhrVX_QQY-hCQlYQ81DWnNpqNWKdEC9OGo8j9TrQg$
> 7. http://www.ks.uiuc.edu/~johns/
> 8. http://www.ks.uiuc.edu/Research/vmd/
> 9. http://www.ks.uiuc.edu/~johns/
> 10. 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/