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

Francesco Pietra chiendarret at gmail.com
Sat Jan 22 06:34:34 PST 2011


Thanks a lot for the time you spent answering me. That we examine
everything graphically, sphere included, is our standard routine, in
particular the various sphere clusters I alluded to. My post was to
show how things run (or not run) and the very reason for posting was
the last sentence:

""Finally, why "When you have spheres in multiple pockets dock may try
and orient the ligand to spheres located in different pockets causing
the ligand to be placed in a vary unfavorable position and pruned
leaving you with no orients"? Is that still inadequacy of the code
(something that could be fixed) or that is a more serious issue?""

which perhaps escaped attention. What I would aim to know is whether
these are limitations (I have just transcribed limitations that you
pointed out before, using just your words) by the code, limitations
that could be fixed, or what I would like to do is beyond the
capability of the code.

I have now checked the autodck4 has no such limitations, although its
use of partial charges and grid space pose other problems.

thanks
francesco pietra

On Sat, Jan 22, 2011 at 2:30 PM, Trent E. Balius <tbalius at aol.com> wrote:
> See manual for discussion of the spheres:
>
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#SphgenOverview
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#SphgenOutput
>
> Here is an excerpt from the SphgenOverview section:
>
> "These sets, or clusters, are sorted according to numbers of constituent
> spheres, and written out in order of descending size. The largest cluster is
> typically the ligand binding site of the receptor molecule. The program
> showsphere writes out sphere center coordinates in PDB format and may be
> helpful for visualizing the clusters (see showsphere)."
>
> Here is an excerpt from the discussion in the SphgenOutput section of the
> manual
>
> "
> The clusters are listed in numerical order from largest cluster found to the
> smallest. At the end of the clusters is cluster number 0. This is not an
> actual sphere cluster, but a list of allof the spheres generated whose radii
> were larger than the minimum radius, before the filtering heuristics ( i.e.,
> allowing only one sphere per atom and using a maximum radius cutoff) and
> clustering were performed. Cluster 0 may be useful as a starting point for
> users who want to explore a wider range of possible clusters than is
> provided by the standard sphgen clustering routine.
> "
>
> When things start not working it is always a good idea to visualize
> everything with a molecular viewing program like Chimera.
>
> Cluster 0 should cover the whole receptor. Other clusters should be specific
> to a pocket as defined by the spacial clustering of the spheres.
>
> I strongly encourage you to visualize the clusters on your protein with
> chimera or your favorite program to see the differences. Show the grid box
> as well.
>
> Segmentation faults are always extremely frustrating.
>
> I am not an expert on amberscore, but I am not sure why you can't compare
> things docked to multipule sphere sets as long as you use the same
> receptor/grid.
>
>
> Good luck and I hope this helps,
>
> Trent
>
> -----Original Message-----
> From: Francesco Pietra <chiendarret at gmail.com>
> To: Trent E. Balius <tbalius at aol.com>
> Sent: Sat, Jan 22, 2011 2:44 am
> Subject: Re: [Dock-fans] Fwd: grid size (former "parameters" and "very large
> receptors")
>
> On Fri, Jan 21, 2011 at 3:45 PM, Trent E. Balius <tbalius at aol.com> wrote:
>
>
>> I would try test #3 from my earlier email.  When you have spheres in
>
>
>> multiple pockets dock may try and orient the ligand to spheres located in
>
>
>> different pockets causing the ligand to be placed in a vary unfavorable
>
>
>> position and pruned leaving you with no orients.
>
>
>>
>
>
>> As a test:
>
>
>>
>
>
>> Use the program showsphere to create a pdb of the spheres.
>
>
>>
>
>
>> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Showsphere
>
>
>>
>
>
>> Visualize the big sphere set with your protein with a program like
>> chimera.
>
>
>> Choose the a reduced set in one pocket and try docking.  Do, say, 5 more
>
>
>> iterations where you increase sphere to increase coverage of the protein.
>
>
>
>
>
> For the moment I have taken a shorter route, i.e., trying
>
>
> anchor_and_grow - in its full exploitation - with the smallest ligands
>
>
> of the family of A31 (the one that caused segmentation fault) and with
>
>
> same settings, i.e. spheres covering the whole receptor and grid 0.6.
>
>
> The smaller ligand (which has rotatables) are treated without
>
>
> problems.
>
>
>
>
>
> It seems to me that the conditions used for these dockings are at the
>
>
> minimum needed to have a reliable score over the whole receptor (I had
>
>
> already tried to explore the receptor in portions; that worked as far
>
>
> as anchor_and_grow and, say, amberscore, are concerned, but there was
>
>
> no way to put together reliably the score for the different portions
>
>
> of the receptor. I make an example: if the smallest ligand is docked
>
>
> over the whole receptor, I get docking  on the "head" of the receptor.
>
>
> If docking is carried out on two different portions of the receptor,
>
>
> "head" and "legs", the same ligand is docked on both. Obviously I
>
>
> can't compare amberscore for the "head" docking with the one for
>
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> "legs".
>
>
>
>
>
> Then I tried another ligand (when I say "ligand" I mean molecules that
>
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> are known to alter the behavior of the protein but it is unknown where
>
>
> they interfere or bind) slightly  less complex that A31, getting again
>
>
> segmentation fault at the stage of orientation:
>
>
>
>
>
> VERBOSE MOLECULE STATS
>
>
>
>
>
>   Number of heavy atoms = 29
>
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>   Number of rotatable bonds = 1
>
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>   Formal Charge = 0.00
>
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>   Molecular Weight = 381.52
>
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>   Heavy Atoms = 29
>
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> Orienting 27 anchor heavy atom centers
>
>
>
>
>
> *******************
>
>
> I have examined the thread you had with Kit. There is something
>
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> unclear to me. You suggest to start from cluster 0 if aimed at blind
>
>
> docking. In my case;
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>
> cluster #.......sphere #
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> 1                  1156
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> 2                   415
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> .........................
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> 0                34623
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> Thus, cluster 0 is the most populated, and the spheres cover the whole
>
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> receptor. I did not even try anchor_and_grow with cluster 0. I
>
>
> understand that your suggestion to start from cluster 0 was to Kit,
>
>
> not to me, but the two problems are not much different.
>
>
> *********************
>
>
>
>
>
> Probably there is something that I did not grasp, but your suggestion
>
>
> to me to start with selected pockets, at the moment does not seem to
>
>
> bring me to the harbor. If I can't compare reliably all the molecules
>
>
> that are known to interfere with the protein, docking simulation will
>
>
> tend to beguile nature, which will turn into beguiling onself.
>
>
>
>
>
> Finally, why "When you have spheres in multiple pockets dock may try
>
>
> and orient the ligand to spheres located in different pockets causing
>
>
> the ligand to be placed in a vary unfavorable position and pruned
>
>
> leaving you with no orients"? Is that still inadequacy of the code
>
>
> (something that could be fixed) or that is a more serious issue?
>
>
>
>
>
> Thanks a lot for your advice
>
>
> francesco pietra
>
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>>
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>> I hope this helps,
>
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>>
>
>
>> 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/
>
>
>>
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>>
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>
>> -----Original Message-----
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>
>> From: Francesco Pietra <chiendarret at gmail.com>
>
>
>> To: Trent E. Balius <tbalius at aol.com>
>
>
>> Sent: Thu, Jan 20, 2011 4:54 pm
>
>
>> Subject: Re: [Dock-fans] Fwd: grid size (former "parameters" and "very
>> large
>
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>> receptors")
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>> I have now tried anchor_and_grow for the same ligand (30 heavy atoms)
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>> with an even coarser grid (0.6) made of only 8,726,355 points. Out
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>> Orienting 28 anchor heavy atom centers
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>> Then I tried anchor_and_grow for methane, same receptor, same grid
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>> -----------------------------------
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>>  Elapsed time for docking:  4 seconds
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>>  Orientations:      395
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>> For curiosity I examined autodock4: to create a box for the whole my
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>> receptor, the grid space needs to be as large as 1A. I did not try if
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>> docking worked for my 30-heavy-atoms molecule.
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>> Well, any comment would be appreciated
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>> francesco pietra
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>> On Tue, Jan 18, 2011 at 2:52 PM, Trent E. Balius <tbalius at aol.com> wrote:
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>>> Hi Francisco,
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>>> As I am interested to work with the whole energy of the receptor
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>>> Even if the grid box does not contain the whole receptor the energy
>>> stored
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>>> at each grid point is calculated from the entire receptor.
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>>>
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>>> That being said I understand that you want to dock all over receptor
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>>> surface.
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>>> I guess you believe that this is a problem with the orienting code?
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>>> It looks like you are docking a rigid molecule.
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>>> Possible tests:
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>>>
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>>> (1) Perform a single point calculation on the grid to demonstrate that it
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>>> is
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>>> not a grid energy problem.
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>>>
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>>> (2) Preform only orienting (no minimization and no growth, make sure that
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>>> your pruning cut off is vary high).  visualize the orients with receptor
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>>> and
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>>> spheres.
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>>>
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>>> (3) Dock with reduced sphere sets, all spheres located in the same
>>> pocket.
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>>> Gradually increase the sphere set to include more spheres within other
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>>> pockets about the protein.
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>>>
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>>> Let us of know of your progress with is problem.  Blind docking is a
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>>> useful
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>>> application of DOCK.
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>>> See the following for previous blind docking discussion:
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>>> http://mailman.docking.org/pipermail/dock-fans/2010-July/002398.html
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>>>
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>>> I hope that these test suggestions help.
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>>>
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>
>>> Trent E. Balius
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>
>>> Graduate Student, Rizzo Group,
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>
>>> Department of Applied Mathematics and Statistics,
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>
>>> Stony Brook University.
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>
>>> Office: Math Tower 3-129, Phone: (631) 632-8519
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>>> URL: http://www.ams.sunysb.edu/~tbalius/
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>>>
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>>>
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>
>>> -----Original Message-----
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>
>>> From: Francesco Pietra <chiendarret at gmail.com>
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>
>>> To: dock-fans <dock-fans at docking.org>
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>
>>> Sent: Tue, Jan 18, 2011 5:32 am
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>
>>> Subject: [Dock-fans] Fwd: grid size (former "parameters" and "very large
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>
>>> receptors")
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>>>
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>
>>> Forgot to add that I have also put in my .bashrc the statement
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>>>
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>>>
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>>>
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>>>
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>>> ulimit -s unlimited
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>>>
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>>>
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>>>
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>>> (Debian GNU/LINUX amd64)
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>>>
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>>>
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>>>
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>>>
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>>>
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>
>>> ---------- Forwarded message ----------
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>>>
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>
>
>>> From: Francesco Pietra <chiendarret at gmail.com>
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>>>
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>
>>> Date: Tue, Jan 18, 2011 at 8:53 AM
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>>> Subject: grid size (former "parameters" and "very large receptors")
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>>> To: dock-fans <dock-fans at docking.org>
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>>> Hello:
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>>> I am combining here my two former threads "vdw parameters" and "very
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>>> large receptors".
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>>> That about the vdw parameters was a wrong message by dock6.4.
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>>> Actually. it was the format. To fit the MW code, the correct format is
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>>> (i.e., C.3, H, etc). The one I got from dockprep in latest version of
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>>> chimera was no good (c3, hc ...)
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>>> @<TRIPOS>ATOM
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>>>      1 C           2.5960   -1.2050    1.7710 C.3       1 A31   -0.0961
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>>>      2 H           2.6980   -1.2650    0.6640 H         1 A31    0.0407
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>>> That corrected, the problem is the grid size. This is a portion of
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>>> anchor_and_grow.out:
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>>>
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>>> Initializing Library File Routines...
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>>> Initializing Orienting Routines...
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>>>
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>
>>> Read in 3433 spheres for orienting.
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>>>
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>>>
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>>> Initializing Conformer Generator Routines...
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>>>
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>>> Initializing Grid Score Routines...
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>>>
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>
>>>  Reading the energy grid from
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>>>
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>>>
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>>>
>
>
>>>
>>> /home/francesco/work_hasic1a_mod21-model/mod21_reduce/grid.whole.0.5/grid.nrg
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>>>  Done reading the energy grid.
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>>>
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>>> -----------------------------------
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>>>
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>>> VERBOSE MOLECULE STATS
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>>>
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>>>
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>>>  Number of heavy atoms = 30
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>>>  Number of rotatable bonds = 1
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>>>  Formal Charge = -0.00
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>>>
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>
>>> Molecular Weight = 383.56
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>>>  Heavy Atoms = 30
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>>>
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>>> Orienting 28 anchor heavy atom centers
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>>>
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>
>>> At this point it crashes, the screen reporting "segmentation fault",
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>>>
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>>>
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>
>>> which per se tells nothing useful. However, contrary to previous
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>>>
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>>>
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>
>>> erroneous messages, it seems to me that it is not a problem of out of
>
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>>>
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>
>
>>> memory. I tried also on a shared-memory machine with a lot of RAM,
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>>>
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>>>
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>
>>> getting exactly the same error message.
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>>>
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>>>
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>
>
>>> It seems to me that dock6.4 is unable to deal with 3433 spheres (which
>
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>>>
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>
>
>>> was to cover the whole receptor at grid space 0.5). I tried now
>
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>>>
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>>>
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>
>
>>> anchor_and_grow with a smaller system investigated in the past with
>
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>>>
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>>>
>
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>
>
>>> previous versions of dock and it was finely completed by my present
>
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>>>
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>>>
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>
>
>>> installation of dock6.4, even on a machine with only 8GB RAM.
>
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>>>
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>>>
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>>>
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>>>
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>>>
>
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>
>>
>
>
>>> As I am interested to work with the whole energy of the receptor, and
>
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>>>
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>>>
>
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>
>
>>> I can't use dock3.5 for the reasons that John pointed out, I would be
>
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>>>
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>>>
>
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>
>>
>
>
>>> happy to have the response of dock6.4 developers, if they agree or not
>
>
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>>>
>
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>>>
>
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>
>>
>
>
>>> with my above conclusions. As always, I am prone to carry out tests on
>
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>>>
>
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>>>
>
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>
>
>>> their suggestions. This is not to limit interventions by
>
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>>>
>
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>>>
>
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>
>
>>> non-developers may have the right ideas about.
>
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>>>
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>>>
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>>>
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>>>
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>>>
>
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>
>
>>> Thanks
>
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>>>
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>>>
>
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>
>>
>
>
>>> francesco pietra
>
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>>>
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>>>
>
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>
>
>>> _______________________________________________
>
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>>>
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>>>
>
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>>
>
>
>>> Dock-fans mailing list
>
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>>>
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>>>
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>
>
>>> Dock-fans at mailman.docking.org
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>>>
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>>> http://mailman.docking.org/mailman/listinfo/dock-fans
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>> _______________________________________________
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>> Dock-fans mailing list
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>> Dock-fans at mailman.docking.org
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>> http://mailman.docking.org/mailman/listinfo/dock-fans
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