VMD-L Mailing List

From: Mary Lowe (mlowe_at_loyola.edu)
Date: Fri Mar 23 2007 - 21:40:18 CDT

Hello,
I would like to read a pdb file, but I get the following error message:

vmd > Info) Using plugin pdb for structure file /Users/mary/CHARMM/arab6001_fix.pdb
Info) Using plugin pdb for coordinates from file /Users/mary/CHARMM/arab6001_fix.pdb
Info) Determining bond structure from distance search ...
VMD(27128,0xa000ed68) malloc: *** vm_allocate(size=996216832) failed (error code=3)
VMD(27128,0xa000ed68) malloc: *** error: can't allocate region
VMD(27128,0xa000ed68) malloc: *** set a breakpoint in szone_error to debug
Segmentation fault

The file contains water molecules of which a few have evaporated. I rewrote the coordinates of the evaporated molecules so that they look like they are still present in the main structure.

Can you explain what the error message means and how to correct the problem? Thanks.