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

Trent E. Balius tbalius at aol.com
Tue Jan 18 05:52:41 PST 2011

 Hi Francisco,

As I am interested to work with the whole energy of the receptor

Even if the grid box does not contain the whole receptor the energy stored at each grid point is calculated from the entire receptor.  

That being said I understand that you want to dock all over receptor surface.  

I guess you believe that this is a problem with the orienting code?

It looks like you are docking a rigid molecule. 

Possible tests: 

(1) Perform a single point calculation on the grid to demonstrate that it is not a grid energy problem.

(2) Preform only orienting (no minimization and no growth, make sure that your pruning cut off is vary high).  visualize the orients with receptor and spheres.   

(3) Dock with reduced sphere sets, all spheres located in the same pocket.  Gradually increase the sphere set to include more spheres within other pockets about the protein.

Let us of know of your progress with is problem.  Blind docking is a useful application of DOCK.  

See the following for previous blind docking discussion:


I hope that these test suggestions help.

Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/



-----Original Message-----
From: Francesco Pietra <chiendarret at gmail.com>
To: dock-fans <dock-fans at docking.org>
Sent: Tue, Jan 18, 2011 5:32 am
Subject: [Dock-fans] Fwd: grid size (former "parameters" and "very large receptors")

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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