Dear Allen,<div>Thank you for your explanation.</div><div><br></div><div>Chinh<span></span><br><br>On Friday, March 22, 2013, William Joseph Allen wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Chinh,<br><br>You did not do anything wrong - the "conformers.mol2" will give you all of the successfully-grown conformers up to the number you specify with "num_scored_conformers". The fact that only 22 were written to file likely means that DOCK could only generate 22 complete molecule conformers that were not pruned away (e.g. because of clashes or bad score).<br>
<br>Joe Allen<br><br><br><br><div class="gmail_quote">On Fri, Mar 22, 2013 at 5:50 AM, Chinh Su Tran To <span dir="ltr"><<a href="javascript:_e({}, 'cvml', 'chinh.sutranto@gmail.com');" target="_blank">chinh.sutranto@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear DOCK-fans,<div><br></div><div>I need to increase the number of docked ligand conformations to 100 (from the 1st trial of 10), so I adjusted the "num_scored_conformers" to 100, but the results "conformers.mol2" only showed 22.</div>
<div>How could that be? or Did I do something wrong?</div><div><br></div><div>Below is my <a href="http://dock.in" target="_blank">dock.in</a>. Would anyone please help take a look?</div><div><br></div><div><div><i>ligand_atom_file ../data/lig.mol2</i></div>
<div><i>limit_max_ligands no</i></div><div><i>skip_molecule no</i></div><div><i>read_mol_solvation no</i></div>
<div><i>calculate_rmsd no</i></div><div><i>use_database_filter no</i></div><div><i>orient_ligand yes</i></div>
<div><i>automated_matching yes</i></div><div><i>receptor_site_file ./rec.sph</i></div><div><i>max_orientations 500</i></div>
<div><i>critical_points no</i></div><div><i>chemical_matching no</i></div><div><i>use_ligand_spheres no</i></div>
<div><i>use_internal_energy yes</i></div><div><i>internal_energy_rep_exp 12</i></div><div><i>flexible_ligand yes</i></div>
<div><i>user_specified_anchor no</i></div><div><i>limit_max_anchors no</i></div><div><i>min_anchor_size 40</i></div>
<div><i>pruning_use_clustering yes</i></div><div><i>pruning_max_orients 100</i></div><div><i>pruning_clustering_cutoff 100</i></div>
<div><i>pruning_conformer_score_cutoff 25.0</i></div><div><i>use_clash_overlap no</i></div><div><i>write_growth_tree no</i></div>
<div><i>bump_filter no</i></div><div><i>score_molecules yes</i></div><div><i>contact_score_primary yes</i></div>
<div><i>contact_score_secondary no</i></div><div><i>contact_score_cutoff_distance 4.5</i></div><div><i>contact_score_clash_overlap 0.75</i></div>
<div><i>contact_score_clash_penalty 50</i></div><div><i>contact_score_grid_prefix grid</i></div><div><i>grid_score_secondary no</i></div>
<div><i>multigrid_score_secondary no</i></div><div><i>dock3.5_score_secondary no</i></div><div><i>continuous_score_secondary no</i></div>
<div><i>descriptor_score_secondary no</i></div><div><i>gbsa_zou_score_secondary no</i></div><div><i>gbsa_hawkins_score_secondary no</i></div>
<div><i>SASA_descriptor_score_secondary no</i></div><div><i>amber_score_secondary no</i></div><div><i>minimize_ligand yes</i></div>
<div><i>minimize_anchor yes</i></div><div><i>minimize_flexible_growth yes</i></div><div><i>use_advanced_simplex_parameters no</i></div>
<div><i>simplex_max_cycles 1</i></div><div><i>simplex_score_converge 0.1</i></div><div><i>simplex_cycle_converge 1.0</i></div>
<div><i>simplex_trans_step 1.0</i></div><div><i>simplex_rot_step 0.1</i></div><div><i>simplex_tors_step 10.0</i></div>
<div><i>simplex_anchor_max_iterations 500</i></div><div><i>simplex_grow_max_iterations 500</i></div><div><i>simplex_grow_tors_premin_iterations 0</i></div>
<div><i>simplex_random_seed 0</i></div><div><i>simplex_rest</i></div></div>_______________________________________________<br>
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<br></blockquote></div><br><br clear="all"><br>-- <br>William Joseph Allen, Ph.D.<br>Postdoctoral Associate<br>Dept. of Applied Mathematics and Statistics<br>Stony Brook University<br><a href="http://ringo.ams.sunysb.edu/~wjallen/" target="_blank">http://ringo.ams.sunysb.edu/~wjallen/</a><br>
</blockquote></div>