VMD-L Mailing List

From: Mike McCallum (mmccallum_at_PACIFIC.EDU)
Date: Tue Oct 19 2021 - 16:33:31 CDT

Thank you, John! We have been seeing a bug in psfgen recently (which we may work around by manually building in the tkcon). I’m anxious to try this new version.

Mike McCallum
mmccallum_at_pacific.edu
cmccallum_at_mac.com
cmikemccallum_at_gmail.com

> On Oct 19, 2021, at 2:19 PM, John Stone <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
>> 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/
>