VMD-L Mailing List

From: miyatake (miyatake_at_riken.jp)
Date: Thu Jul 02 2020 - 22:09:01 CDT

Dear VMD users,

I installed these two apps in my MacBookPro16 (10.15.5);

VMD 1.9.4a43 Rev 6 for MacOS X Catalina
NAMD 2.14b1

Then, I opened QwikMD, and click "Prepare" but it did not work and clashed
showing the logs below;

Does anyone have an idea how to resolve the problem?

                   Miyatake

Step 3 done
Info) Using plugin pdb for structure file Test11_formatted.pdb
Info) Using plugin pdb for coordinates from file Test11_formatted.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 1740
Info) Bonds: 1781
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 313
Info) Waters: 101
Info) Segments: 1
Info) Fragments: 108 Protein: 3 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 Test11_formatted_autopsf-temp.pdb for writing.
Info) Finished with coordinate file Test11_formatted_autopsf-temp.pdb.
Reading PDB CONECT records...
Info) Opened coordinate file Test11_formatted_autopsf-temp.xbgf for writing.
Info) Finished with coordinate file Test11_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
/Applications/VMD 1.9.4a43-Catalina-Rev6.app/Contents/MacOS/startup.command: line 7: 2073 Segmentation fault: 11 "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
logout
Saving session...
..copying shared history...
..saving history...truncating history files...
..completed.
Deleting expired sessions...none found.