VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Sep 25 2009 - 07:55:47 CDT

luca,

please always provide information about the version of VMD
and platform that you are running on. you may well run into
a problem that has already been solved or that is due to the
limitations of the platform that you are running. since it will
take considerable effort to reproduce your problems, it would
be nice to be able to rule out certain known problems. thanks

ciao,
    axel.

On Fri, Sep 25, 2009 at 6:40 AM, Luca Gelisio <luca.gelisio_at_gmail.com> wrote:
> 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
>
>
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.