manual.c.html

最经典的分子对结软件

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ligand_atom_file</P>
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Enter the ligand MOL2 file name here (including the directory path if this file is not in the current directory).</P>
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receptor_site_file</P>
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Enter the sphgen site point file name here.</P>
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score_grid_prefix</P>
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Enter the grid file name prefix here.</P>
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<A HREF="Manual.19.html#14299" CLASS="XRef">
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vdw_definition_file</P>
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~dock/parameter/vdw.defn</P>
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&nbsp;</P>
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2E: <A NAME="23767">
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Output</A>
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Keyword</P>
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Suggestions</P>
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ligand_energy_file</P>
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dock_nrg.mol2</P>
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<H3 CLASS="Table">
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Table 3. Recommended beginner's Dock parameters for a database search run</H3>
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3A: Parameters to Modify from Database Run</H3>
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Keyword</P>
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Previous</P>
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Suggestions</P>
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<A HREF="Manual.19.html#37217" CLASS="XRef">
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multiple_ligands</P>
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no</P>
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yes; to consider multiple molecules</P>
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<A HREF="Manual.19.html#32044" CLASS="XRef">
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maximum_orientations</P>
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500</P>
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50; just so that the run doesn't take too long</P>
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<A HREF="Manual.19.html#20966" CLASS="XRef">
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write_orientations</P>
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yes</P>
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no; to write only the best orientation for each molecule</P>
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&nbsp;</P>
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3B: <A HREF="Manual.19.html#17976" CLASS="XRef">
Multiple Ligands</A>
&nbsp;</H3>
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Keyword</P>
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Suggestions</P>
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<A HREF="Manual.19.html#14818" CLASS="XRef">
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parallel_jobs</P>
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no</P>
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<A HREF="Manual.19.html#42533" CLASS="XRef">
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ligands_maximum</P>
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first try 10 to make sure everything is working, then set it to a number larger than the number of molecules in input file</P>
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initial_skip</P>
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0; n&gt;0 will skip the first n molecules in input file</P>
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interval_skip</P>
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0; n&gt;0 will skip n molecules for each molecule processed</P>
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heavy_atoms_minimum</P>
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4; to discard small molecules</P>
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heavy_atoms_maximum</P>
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50; to discard large molecules</P>
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rank_ligands</P>
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yes; to save a top score list</P>
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rank_ligand_total</P>
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50; to save the top 50 molecules</P>
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restart_interval</P>
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100; to save restart info every 100th molecule processed</P>
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&nbsp;</P>
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3C: Additional <A HREF="Manual.19.html#12854" CLASS="XRef">
Input</A>
 and <A HREF="Manual.c.html#23767" CLASS="XRef">
Output</A>
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Keyword</P>
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Suggestions</P>
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quit_file</P>
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dock.quit</P>
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dump_file</P>
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dock.dump</P>
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info_file</P>
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dock.info</P>
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restart_file</P>
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dock.rst</P>
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<P CLASS="Body">
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If you happen to enter the wrong value for any parameter and wish to change it, then you may edit the dock.in file directly and modify the parameter value.  Once all parameters have been entered, dock should begin the calculation and the dock.in file is complete.  You may kill the process with a CTRL-C and relaunch the process in background by typing &quot;dock -i dock.in -o dock.out&amp;&quot;.  If you would like to run dock multiple times from the same directory, then you may use a different name for dock.in and dock.out.  Just be sure to change the names of the output files inside the new dock.in file so that two processes don't end up overwriting each other's output files.</P>
<P CLASS="Body">
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Check a few minutes after you start the run to be sure that it is still going; if it has stopped, look for mistakes in the input. Beginners should check disk usage occasionally while the job is running, just in case the program is creating incredibly large files which might overflow the available space.</P>
<P CLASS="Body">
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During a database search run (which can take anywhere from hours to days to weeks to finish), you can follow dock's progress through the database by inspecting the *.info file.</P>
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Restarting a Search Run</H6>
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In database search mode of dock (when multiple_ligands, orient_ligand, and rank_ligands are selected), dock periodically saves information necessary to restart the search from its current location in the database in a *.rst file.  If there is a power failure or the system crashes, you can set up a new run to start where the last one was stopped.  First, make a copy of dock.out so that status of the previous run are saved. Then relaunch the job using the -r flag at the command line.  (Do not change the remaining files, since dock needs them to restart successfully.)  When the restarted run finishes, the sorted list of ligands in the output file will include the top scorers from the entire database.</P>
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<DIV>
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Looking at the Results</H6>
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Dock puts the resulting molecule orientations in a file for each type of scoring function used.  The scores are given in the comment records at the beginning of each molecule record.  If you have selected MOL2 format for your output files and your graphical viewer does not read this format, then convert the file to PDB by typing dock -i dock_nrg.mol2 -o dock_nrg.pdb.</P>
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<DIV>
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Other Post-Docking Tasks</H6>
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Depending on your particular project, you might be interesting in any one or several of the following post-docking techniques:</P>
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Rescoring of hits with alternative scoring function;</LI>
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Redocking of hits with increased orientation sampling and/or conformational sampling;</LI>
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Similarity searching based on hits; or</LI>
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Further molecular modeling/molecular dynamics/FEP of hits;</LI>
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&nbsp;</H6>
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