Dear <font face="Tahoma" size="2">Sudipto:<br><br>Thanks for the email and the sample input. After comparing with your input with mine, I think I know my problem here. It turned out to be that I should set &quot;</font>cluster_conformations = yes&quot; otherwise dock6 will only write one conformation per molecule. (I have tested this on a set of 5,000 molecules.)<font face="Tahoma" size="2"> Not exactly sure why though, as I originally thought if I set it to no, dock will output the top N poses simply based on the primary score.<br>
</font><br><br>Cen<br><br><div class="gmail_quote">On Fri, Jul 16, 2010 at 1:04 PM, Sudipto Mukherjee <span dir="ltr">&lt;<a href="mailto:sudmukh@yahoo.com">sudmukh@yahoo.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">Dear Cen,<br><br>A maximum of 3 docked conformers will be written to prefix_scored.mol2<br>Nothing will be written to prefix_confomer.mol2 with write_conformations set to no.<br>
<br>In your case, what is happening is that after scoring, pruning and clustering, only one viable docked conformation remains. You will get up to 3 conformations in prefix_scored.mol2 if you keep trying with different ligands. I suggest that try this with a small database of 1000 ligands instead of just docking in one molecule. You should that many of them will have 2 or more conformers in the prefix_scored.mol2 file. <br>
<br>For your reference, here is the dock input file I used to verify this:<br><br><span style="font-family: lucida console,sans-serif;">orient_ligand                                                yes</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">automated_matching                                           yes</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">receptor_site_file                                           121P.rec.clust.close.sph</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">max_orientations                                             1000</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">critical_points                                              no</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">chemical_matching                                            no</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">use_ligand_spheres                                           no</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">use_internal_energy                                          yes</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">internal_energy_rep_exp                                      12</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">flexible_ligand                                              yes</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">min_anchor_size                                              5</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">pruning_use_clustering                                       yes</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">pruning_max_orients                                          1000</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">pruning_clustering_cutoff                                    100</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">pruning_conformer_score_cutoff                              
 100.0</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">use_clash_overlap                                            no</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">print_growth_tree                                            no</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">bump_filter                                                  no</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">score_molecules                                              yes</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">contact_score_primary                                        no</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">contact_score_secondary                                      no</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">grid_score_primary                                           yes</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">grid_score_secondary                                         no</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">grid_score_rep_rad_scale                                     1</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">grid_score_vdw_scale                                         1</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">grid_score_es_scale                                          1</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">grid_score_grid_prefix                                       121P.rec</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">dock3.5_score_secondary                                      no</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">continuous_score_secondary                                   no</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">gbsa_zou_score_secondary                                     no</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">gbsa_hawkins_score_secondary                                 no</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">amber_score_secondary                                        no</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">minimize_ligand                                              yes</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">minimize_anchor                                              yes</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">minimize_flexible_growth                                     yes</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">use_advanced_simplex_parameters                              no</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">simplex_max_cycles                                           1</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">simplex_score_converge                                       0.1</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">simplex_cycle_converge                                       1.0</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">simplex_trans_step                                           1.0</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">simplex_rot_step                                             0.1</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">simplex_tors_step                                            10.0</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">simplex_anchor_max_iterations                                500</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">simplex_grow_max_iterations                                  500</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">simplex_grow_tors_premin_iterations                          0</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">simplex_random_seed                                          0</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">atom_model                                                   all</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">vdw_defn_file                                                vdw_AMBER_parm99.defn</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">flex_defn_file                                               flex.defn</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">flex_drive_file                                              flex_drive.tbl</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">ligand_outfile_prefix                                        flex.dock2grid</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">write_orientations                                           no</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">num_scored_conformers                                        1</span><br style="font-family: lucida console,sans-serif;"><span style="font-family: lucida console,sans-serif;">write_conformations                                          no</span><br style="font-family: lucida console,sans-serif;">
<span style="font-family: lucida console,sans-serif;">rank_ligands                                                 no</span><br><div> </div><font size="2"><span style="font-family: tahoma,new york,times,serif;">Regards<br>
Sudipto Mukherjee<br>Trent E. Balius<br></span></font><div class="im"><font size="2"><span style="font-family: tahoma,new york,times,serif;"><span style="font-style: italic; color: rgb(82, 83, 48);">Graduate Student, Robert C. Rizzo Lab</span><br style="font-style: italic; color: rgb(82, 83, 48);">
<span style="font-style: italic; color: rgb(82, 83, 48);">Dept. of Applied Math &amp; Statistics, Stony Brook University</span><span style="font-style: italic; color: rgb(82, 83, 48);"></span></span></font></div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">
<br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><div class="im"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Cen Gao &lt;<a href="mailto:cengao@gmail.com" target="_blank">cengao@gmail.com</a>&gt;<br>
</div><b><span style="font-weight: bold;">To:</span></b> Sudipto Mukherjee &lt;<a href="mailto:sudmukh@yahoo.com" target="_blank">sudmukh@yahoo.com</a>&gt;<br><b><span style="font-weight: bold;">Cc:</span></b> <a href="mailto:Dock-fans@mailman.docking.org" target="_blank">Dock-fans@mailman.docking.org</a><br>
<b><span style="font-weight: bold;">Sent:</span></b> Thu, July 15, 2010 6:03:42 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [Dock-fans] Write multiple conformations during parallel  processing<br></font><div>
<div></div><div class="h5"><br>
Hi Sudipto:<br><br>Thanks for the email. I have tried to set  &quot;num_scored_conformer&quot; to 3 and &quot;write_conformations&quot; to No before, but it still generated only one pose per molecule to prefix_scored.mol2, while never wrote anything to prefix_confomer.mol2. May I ask whether this setting works differently on your version of DOCK?  (I am using DOCK6.4, compiled with GCC4.1)  Or are there any parameters I should set?<br>

<br>If I set write_conformations to yes, it was able to write 1 pose to prefix_scored.mol2 and 3 poses per molecule into prefix_confomer.mol2 as expected. But again it works in serial version of DOCK only, but refuses to run in parallel.<br>

<br><br>Thanks<br><br><br>Cen<br><br><br><div class="gmail_quote">On Thu, Jul 15, 2010 at 5:21 PM, Sudipto Mukherjee <span dir="ltr">&lt;<a rel="nofollow" href="mailto:sudmukh@yahoo.com" target="_blank">sudmukh@yahoo.com</a>&gt;</span> wrote:<br>
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<div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">Hi Cen,<br><br>As you mentioned in your email, the &quot;num_scored_conformer&quot; is the parameter you want to use. <br>Set this to 3 as you wish. <br>

Set &quot;write_conformations&quot; as no. By default this is yes. The naming convention is a bit confusing here, I admit. The write_conformations parameter writes out partial conformers in a separate conformers.mol2 Setting this parameter to yes is what geenrates the ERROR about filling up the disk during mpi runs. <br>

<br>Now you should have a maximum of 3 conformers for each molecule screened. <br><div> </div><font size="2"><span style="font-family: tahoma,new york,times,serif;">Regards<br>Sudipto Mukherjee<br></span></font><font size="2"><span style="font-family: tahoma,new york,times,serif;"><span style="font-style: italic; color: rgb(82, 83, 48);">Graduate Student,
 Robert C. Rizzo Lab</span><br style="font-style: italic; color: rgb(82, 83, 48);"><span style="font-style: italic; color: rgb(82, 83, 48);">Dept. of Applied Math &amp; Statistics, Stony Brook University</span></span></font><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">

<br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Cen Gao &lt;<a rel="nofollow" href="mailto:cengao@gmail.com" target="_blank">cengao@gmail.com</a>&gt;<br>

<b><span style="font-weight: bold;">To:</span></b> <a rel="nofollow" href="mailto:Dock-fans@mailman.docking.org" target="_blank">Dock-fans@mailman.docking.org</a><br><b><span style="font-weight: bold;">Sent:</span></b> Tue, July 13, 2010 12:13:53 PM<br>

<b><span style="font-weight: bold;">Subject:</span></b> [Dock-fans] Write multiple conformations during parallel processing<br></font><div><div></div><div><br>
Dear Dock fans:<br><br>May I ask is it possible for DOCK to write out the top N conformers for each molecule it processed during the parallel docking run? The manual states that this feature is only available to serial version of DOCK to &quot;protect against filling up the disk&quot;, as &quot;in conformer.mol2, the number of
molecules in the output file will be equal to the database size * the
number of anchors per molecule * the number of conformations that pass
the final pruning stage * the number of conformers per cycle.&quot;  <br><br>But if I understand it right, this conformer number should not be that huge as it is something we can control using the keyword &quot;num_scored_conformer&quot; (in the case of primary_score only), right?  As long as I set this keyword to a smaller value, say 3 or 5, it will only write 3 or 5 poses per molecule, which will not be a problem in case of the file size. Did I miss something here?<br>


<br><br>Thanks<br><br>Cen<br><br>
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