[Dock-fans] Fwd: grid size (former "parameters" and "very large receptors")

Francesco Pietra chiendarret at gmail.com
Tue Jan 18 02:32:26 PST 2011

Forgot to add that I have also put in my .bashrc the statement

ulimit -s unlimited

(Debian GNU/LINUX amd64)

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Tue, Jan 18, 2011 at 8:53 AM
Subject: grid size (former "parameters" and "very large receptors")
To: dock-fans <dock-fans at docking.org>

I am combining here my two former threads "vdw parameters" and "very
large receptors".

That about the vdw parameters was a wrong message by dock6.4.
Actually. it was the format. To fit the MW code, the correct format is
(i.e., C.3, H, etc). The one I got from dockprep in latest version of
chimera was no good (c3, hc ...)

     1 C           2.5960   -1.2050    1.7710 C.3       1 A31   -0.0961
     2 H           2.6980   -1.2650    0.6640 H         1 A31    0.0407

That corrected, the problem is the grid size. This is a portion of

Initializing Library File Routines...
Initializing Orienting Routines...
Read in 3433 spheres for orienting.
Initializing Conformer Generator Routines...
Initializing Grid Score Routines...
 Reading the energy grid from
 Done reading the energy grid.


 Number of heavy atoms = 30
 Number of rotatable bonds = 1
 Formal Charge = -0.00
Molecular Weight = 383.56
 Heavy Atoms = 30
Orienting 28 anchor heavy atom centers

At this point it crashes, the screen reporting "segmentation fault",
which per se tells nothing useful. However, contrary to previous
erroneous messages, it seems to me that it is not a problem of out of
memory. I tried also on a shared-memory machine with a lot of RAM,
getting exactly the same error message.

It seems to me that dock6.4 is unable to deal with 3433 spheres (which
was to cover the whole receptor at grid space 0.5). I tried now
anchor_and_grow with a smaller system investigated in the past with
previous versions of dock and it was finely completed by my present
installation of dock6.4, even on a machine with only 8GB RAM.

As I am interested to work with the whole energy of the receptor, and
I can't use dock3.5 for the reasons that John pointed out, I would be
happy to have the response of dock6.4 developers, if they agree or not
with my above conclusions. As always, I am prone to carry out tests on
their suggestions. This is not to limit interventions by
non-developers may have the right ideas about.

francesco pietra

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