From: Subha Kalyaanamoorthy (skalyaanamoorthy_at_gmail.com)
Date: Wed Nov 09 2022 - 11:36:29 CST

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