Re: segmentation fault

From: Jim Phillips (
Date: Tue Sep 16 2003 - 15:27:10 CDT


I see this error message in your log file:

  Warning: Not all atoms have unique coordinates.

What this really means is that two atoms were unphysically close together
and were treated as being excluded. The likely interpretation is that the
atoms have the same coordinates, probably because they are actually
uninitialized and were set to the default value (0,0,0) by psfgen.

Of course, a segmentation fault shouldn't happen under any circumstance.
Please see if the problem also happens with the just-released 2.5b2.


On Tue, 16 Sep 2003, Cheri M Turman wrote:

> Hi,
> I have been successfully running NAMD on many cytochrome p450s for
> awhile now and for some reason I am getting a segmentation fault on only
> one of the isoforms. The only differences between the runs can only be
> in the psf and pdb files because the .config are the same for all
> proteins I run. I also used the same psfgen utility within NAMD to
> create the psf files so that should not be the problem. The only major
> difference I can see is the cell origin. My other successful protein's
> origins were only + integers and with this problem potein, they are all
> -. Seg faults usually deal with stacksize so I am thinking, does the
> cell origin (-7 -19 -30) cause the program to require more memory? Can
> anyone comment on this and help me out? Also, does anyone know how I
> might recenter the protein and try my hypothesis. I am trying in VMD
> but I haven't got that to work just yet. I am attaching the .log just
> in case.
> Cheers,
> Cheri
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Cheri M. Turman
> Graduate Student
> University of Texas-Houston Medical School
> 6431 Fannin
> Houston, TX 77030
> e-mail:
> Ph.: 713-500-6126
> Fax: 713-500-0652

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