VMD-L Mailing List

From: Luca Gelisio (luca.gelisio_at_gmail.com)
Date: Fri Sep 25 2009 - 05:40:17 CDT

Hi to all,

I'm building a huge Solvation Box (500x500x500), rotating water molecules.
When VMD finishes building I get the following error followed by a
segmentation fault:

> ERROR) Error reading bond information.
> Segmentation fault
>

Here the whole output, from last generated segment:

> building segment W511
> setting patch for first residue to NONE
> setting patch for last residue to NONE
> Info: generating structure...
> Info: segment complete.
> building segment W512
> setting patch for first residue to NONE
> setting patch for last residue to NONE
> Info: generating structure...
> Info: segment complete.
> Info: writing psf file solvate.psf
> total of 12337020 atoms
> total of 8224680 bonds
> total of 4112340 angles
> total of 0 dihedrals
> total of 0 impropers
> total of 0 cross-terms
> Info: psf file complete.
> Info: writing pdb file solvate.pdb
> Info: pdb file complete.
> clearing structure, preserving topology and aliases
> Info) Using plugin psf for structure file solvate.psf
> ERROR) Error reading bond information.
> Segmentation fault
>

Can this error be avoided?

Many thanks,

luca