manual.1e.html

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML EXPERIMENTAL 970324//EN"><HTML><HEAD><META NAME="GENERATOR" CONTENT="Adobe FrameMaker 5.5/HTML Export Filter"><LINK REL="STYLESHEET" HREF="Manual.css"><TITLE> Input Parameters</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-3"><A NAME="pgfId=904"> </A>Input Parameters</H2><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=14175"> </A>File Format</H3><P CLASS="Body"><A NAME="pgfId=14176"> </A>See <A HREF="Manual.19.html#40687" CLASS="XRef">Table 2. on page 55</A> for file format specifications.</P></DIV><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=14184"> </A>Parameters</H3><P CLASS="Body"><A NAME="pgfId=14198"> </A>Like dock, grid should be executed in interactive mode to construct an input file since not all parameters need to be specified for most runs.  After all parameters have been entered, use CTRL-C to kill the process and resubmit it in batch mode using the same input file.</P><H3 CLASS="Table"><A NAME="pgfId=12970"> </A>Table 5. grid input parameters</H3><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=13024"> </A>5A: General Parameters&nbsp;</H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17640"> </A>Parameter</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17642"> </A>Type</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17644"> </A>Default</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17646"> </A>Description</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13001"> </A>compute_grids</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17634"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13003"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13005"> </A>Flag to compute scoring grids.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13007"> </A>grid_spacing</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17636"> </A>real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13009"> </A>0.3</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13011"> </A>The distance between grid points along each axis.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13013"> </A>output_molecule<A NAME="29815"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17638"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13015"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13017"> </A>Flag to write out the coordinates of the receptor into a new, cleaned-up file.  Atoms are resorted to put all residue atoms together.  Terminal sybyl capping groups are merged with the terminal residues.  This option can be useful to fix ligands also, so that hydrogens added by sybyl are put with the proper residue.</P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=908"> </A>&nbsp;</P><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=13621"> </A>5B: Scoring Parameters&nbsp;</H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17620"> </A>Parameter</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17622"> </A>Type</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17624"> </A>Default</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17626"> </A>Description</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13648"> </A>contact_score</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13650"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13652"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13654"> </A>Flag to construct contact grid.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13656"> </A>contact_cutoff_distance<A NAME="19748"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13658"> </A>real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13660"> </A>4.5</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13662"> </A>Maximum distance between heavy atoms for the interaction to be counted as a contact.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13682"> </A>chemical_score<A NAME="35044"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13684"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13686"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13688"> </A>Flag to construct chemical grid.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13690"> </A>energy_score</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13692"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13694"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13696"> </A>Flag to perform energy scoring.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13698"> </A>energy_cutoff_distance<A NAME="35944"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13700"> </A>real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13702"> </A>10</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13704"> </A>Maximum distance between two atoms for their contribution to the energy score to be computed. </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13761"> </A>atom_model<A NAME="33172"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13763"> </A>string</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13765"> </A>u</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13767"> </A>Flag for how to model of non-polar hydrogens.</P><UL><LI CLASS="Bullet"><A NAME="pgfId=13768"> </A>u = United atom model.  Hydrogens attached to carbons are assigned a zero VDW well-depth and the partial charge is transferred to the carbon.</LI><LI CLASS="Bullet"><A NAME="pgfId=13769"> </A>a = All atom model.  Hydrogens attached to carbons have regular VDW well-depth and partial charge is not modified.</LI></UL></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13779"> </A>attractive_exponent<A NAME="12372"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13781"> </A>integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13783"> </A>6</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13785"> </A>Exponent of attractive Lennard-Jones term for VDW potential.  See <A HREF="Manual.1c.html#29459" CLASS="XRef">Equation 1 on page 74</A> for context.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13771"> </A>repulsive_exponent<A NAME="24040"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13773"> </A>integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13775"> </A>12</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13777"> </A>Exponent of repulsive Lennard-Jones term for VDW potential.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13706"> </A>distance_dielectric<A NAME="33818"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13708"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13710"> </A>yes</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13712"> </A>Flag to make the dielectric depend linearly on the distance.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13714"> </A>dielectric_factor<A NAME="24740"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13716"> </A>real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13718"> </A>4</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13720"> </A>Coefficient of the dielectric.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13748"> </A>bump_filter</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13750"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13752"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13754"> </A>Flag to screen each orientation for clashes with receptor prior to scoring and minimizing.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13795"> </A>bump_overlap<A NAME="23822"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13797"> </A>real</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13799"> </A>0.75</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13815"> </A>Amount of VDW overlap allowed.  If the probe atom and the receptor heavy atom approach closer than this fraction of the sum of their VDW radii, then the position is flagged as a bump.</P><UL><LI CLASS="Bullet"><A NAME="pgfId=13816"> </A>0 = Complete overlap allowed.</LI><LI CLASS="Bullet"><A NAME="pgfId=13801"> </A>1 = No overlap allowed.</LI></UL></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=13352"> </A>&nbsp;</P><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=13836"> </A>5C: <A NAME="13109"> </A>File Input&nbsp;</H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17608"> </A>Parameter</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17610"> </A>Default</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17612"> </A>Description</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13857"> </A>receptor_file</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13859"> </A>receptor.mol2</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13861"> </A>Receptor coordinate file.  Partial charges and atom types need to be present.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13863"> </A>box_file</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13865"> </A>site_box.pdb</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13867"> </A>File containing <A HREF="Manual.3d.html#28340" CLASS="XRef">showbox</A> output file which specifies boundaries of grid.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13869"> </A>vdw_definition_file<A NAME="22067"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13871"> </A>$PATH/vdw.defn</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13873"> </A>VDW parameter file.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13906"> </A>chemical_definition_file</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13908"> </A>$PATH/chem.defn</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13910"> </A>Chemical label definition file for use when <A HREF="Manual.1e.html#35044" CLASS="XRef">chemical_score</A> set.</P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=13353"> </A>&nbsp;</P><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=13923"> </A>5D: <A NAME="38720"> </A>File Output</H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17614"> </A>Parameter</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17616"> </A>Default</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17618"> </A>Description</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13944"> </A>score_grid_prefix</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13946"> </A>grid</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13948"> </A>Core file name of grids (file extension will be appended automatically).</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=13950"> </A>receptor_out_file</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13952"> </A>receptor_out.mol2</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=13954"> </A>File for cleaned-up receptor when <A HREF="Manual.1e.html#29815" CLASS="XRef">output_molecule</A> set.</P></TD></TR></TABLE></DIV><CENTER><P>

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