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Create rec.pdb and xtal-lig.mol2 for the receptor and the ligand, and type: You can sometimes start from as little as a [[PDB]] file using [[be_blasti]].

This format is used for general molecule input and output of DOCK. Although previous versions of DOCK supported an extended PDB forma ...the SOLVATION record, that has the atomic desolvation information for the ligand atoms. The parameter read_mol_solvation can be used to read in this record.

This page describes simple protocols for receptor/active site and ligand minimization using Plop.<br> ..._hydrogens_to_your_ligand_and_convert_to_mol2_format Add hydrogens to your ligand and convert to mol2 format]

...ioactive conformation to get a score for the crystallographic pose of your ligand. This is described here: http://wiki.uoft.bkslab.org/index.php/Scoreopt [[File:Nz14 xtal vs dock.png|thumb|right|alt=Prediction by DOCK depicted in yellow

$ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A

...ocking. Mabye you want to increase the number of conformations sampled per ligand, or the force field used.<br> ...opy a file called omega.parm into the directory where you want to generate ligand conformations using dbgen.csh. You should find a template in $DOCK_BASE/dat

* Full dependency resolution means you can change any input or parameter file and type 'make' to generate all files that depend on that change (i.e. tart # rec.pdb: Prepared receptor file

=Ligand File Input= Before you can dock a ligand, you will need atom

...>', which you can read into ViewDOCK in chimera as a DOCK 4, 5, or 6 style file. ...run <tt>$mud/topdock.py -e</tt>. If one wants to create an <tt>.eel1</tt> file for a different subset of the molecules, first create the list of molecule

=Preparing a ligand= *the file containing the [http://www.daylight.com/smiles/ SMILES] strings should cont

...ed for interpolating the electrostatic potential from the phimap on to the ligand position. INPUT FILE:

...ocking. Mabye you want to increase the number of conformations sampled per ligand, or the force field used.<br> ...opy a file called omega.parm into the directory where you want to generate ligand conformations using dbgen.csh. You should find a template in $DOCK_BASE/dat

DOCK 3.6 Ligand Clustering * Example INDOCK file parameters, add to your current INDOCK file

The filename should be a file that contains PDB codes you want to download. ...et a rec.pdb (representing the protein) and xtal-lig.pdb (representing the ligand or a set of atoms in the binding site of the protein) (these names can be c

...file. blastermaster.py described on the [[Dock3.7]] page writes an INDOCK file for you, which you can modify. # OUTPUT

...implementation avoids bin boundaries that prevent some receptor sphere and ligand atom pairs from matching, and, as a result, it can find good matches missed There are two types of ligand orientation currently available:

== Prepare “SMILES ID” file. == * Second arg: input smi file

...he generation of a specific docking configuration for a given receptor and ligand. First you need to create the file structure for your blastermaster job. To do so, simply type

DOCK3.7 is a new version of DOCK, with new accessory tools for protein & ligand preparation as well. The website for download will eventually be: http://d ''Ligand Preparation''

boundaries that prevent some receptor sphere and ligand atom pairs from There are two types of ligand