VMD-L Mailing List

From: Subha Kalyaanamoorthy (skalyaanamoorthy_at_gmail.com)
Date: Mon Oct 30 2023 - 11:01:09 CDT

Hi There,

Everytime, I open a protein-ligand complex file to run the autopsf builder,
VMD crashes. I am using VMD1.9.4a55 on MacOS v11.7.10 (Big sur).

I am attaching the sample files and the RTF files generated from
Swissparam. I have tested the autopsf builder with different protein-ligand
complexes and using the topology files generated through different ways,
but VMD crashes with every protein-ligand autopsf run.

In the log, I see that it mentions unknown residue BNZ, but I have the rtf
file added for the residue in the autopsf. I am not sure if the malloc
error is due to memory issues or because of not being able to read the
uploaded rtf files.

Any help to fix this would be appreciated.

----------

segment complete.

psfgen) reading coordinates from pdb file 4w52_pl_autopsf-temp.pdb_AP1.pdb
for segment AP1

psfgen) Warning: failed to set coordinate for atom O LEU:164 AP1

segfiles 4w52_pl_autopsf-temp.pdb_AP1.pdb 4w52_pl_autopsf-temp.pdb_AO1.pdb

4w52_pl_autopsf-temp.pdb_AO1.pdb

1288 1307

psfgen) building segment AO1

psfgen) reading residues from pdb file 4w52_pl_autopsf-temp.pdb_AO1.pdb

psfgen) unknown residue type BNZ

psfgen) unknown residue type EPE

psfgen) extracted 2 residues from pdb file

psfgen) setting patch for first residue to none

psfgen) setting patch for last residue to none

Info: generating structure...

psfgen) unknown residue type BNZ

VMD(1767,0x112cc3e00) malloc: *** error for object 0x7f88f63c2d60: pointer
being freed was not allocated

VMD(1767,0x112cc3e00) malloc: *** set a breakpoint in malloc_error_break to
debug

/Users/Subha/Desktop/VMD
1.9.4a55-x86_64-Rev11.app/Contents/MacOS/startup.command: line 7: 1767
Abort trap: 6 "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*

logout

-n Savi

 --------
Thanks,
Subha