VMD-L Mailing List
From: Subha Kalyaanamoorthy (skalyaanamoorthy_at_gmail.com)
Date: Wed Nov 09 2022 - 11:36:29 CST
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Hi There,
Everytime, I open a small molecule or run an autopsf builder for a ligand
complex, VMD crashes. I am using VMD1.9.4a55 on MacOS (Big sur)
Is there a fix available for this?
---------------
Info) Using plugin mol2 for structure file
/Users/SK/Desktop/4dqb_D_017/4dqb_D_017.mol2
Info) Using plugin mol2 for coordinates from file
/Users/SK/Desktop/4dqb_D_017/4dqb_D_017.mol2
Info) Analyzing structure ...
Info) Atoms: 75
Info) Bonds: 78
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 1
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 0 Nucleic: 0
Info) Finished with coordinate file
/Users/SK/Desktop/4dqb_D_017/4dqb_D_017.mol2.
Info) Opened coordinate file 4dqb_D_017_autopsf_preformat_protein.pdb for
writing.
Info) Finished with coordinate file
4dqb_D_017_autopsf_preformat_protein.pdb.
Info) Opened coordinate file 4dqb_D_017_autopsf_preformat_glycan.pdb for
writing.
Info) Finished with coordinate file 4dqb_D_017_autopsf_preformat_glycan.pdb.
Info) Analyzing structure ...
Info) Atoms: 75
Info) Bonds: 78
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 1 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 1
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 0 Nucleic: 0
Info) Opened coordinate file 4dqb_D_017_autopsf_preformat_other.pdb for
writing.
Info) Finished with coordinate file 4dqb_D_017_autopsf_preformat_other.pdb.
Info) Opened coordinate file 4dqb_D_017_autopsf_preformat_ion.pdb for
writing.
Info) Finished with coordinate file 4dqb_D_017_autopsf_preformat_ion.pdb.
Info) Opened coordinate file 4dqb_D_017_autopsf_preformat_water.pdb for
writing.
Info) Finished with coordinate file 4dqb_D_017_autopsf_preformat_water.pdb.
Info) Using plugin pdb for structure file 4dqb_D_017_autopsf_formatted.pdb
Info) Using plugin pdb for coordinates from file
4dqb_D_017_autopsf_formatted.pdb
VMD(55052,0x5f5080) malloc: can't allocate region
*** mach_vm_map(size=2283634688) failed (error code=3)
VMD(55052,0x5f5080) malloc: *** set a breakpoint in malloc_error_break to
debug
/Users/SK/Desktop/VMD 1.9.4.app/Contents/MacOS/startup.command: line 7:
55052 Segmentation fault: 11 "$p/../Resources/VMD.app/Contents/MacOS/VMD"
$*
logout
Saving session...
..copying shared history...
..saving history...truncating history files...
..completed.
-----------------
Thanks,
Subha
- Next message: Stefan Lyne Oliver: "RE: RE: Simple MDFF Tutorial - 1ake does not fit into map"
- Previous message: utku.ozkan_at_bilkent.edu.tr: "Re: Topotools "guessangles" not assigning angles"
- Next in thread: John Stone: "Re: MacOS VMD1.9.4.a55 crashes- malloc: can't allocate region"
- Reply: John Stone: "Re: MacOS VMD1.9.4.a55 crashes- malloc: can't allocate region"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
