From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 09 2022 - 19:36:57 CST

Hi,
  Can you send me an example of some of mol2 files that you're loading that
are causing the problem you describe? Most likely there's an issue of
some kind with the mol2plugin, and having a copy of some of the files that
trigger trouble would make it easy to run in a debugger and ultimately to
resolve.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Nov 09, 2022 at 12:36:29PM -0500, Subha Kalyaanamoorthy wrote:
> 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

-- 
Research Affiliate, 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/           
http://www.ks.uiuc.edu/Research/vmd/