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...is stored for each grid element in the active site. Thus the volume based ligand desolvation energy is calculated as: Here L is the ligand atom desolvation, volume summed over k volume elements, V. This method is o

...ed into the output. If a parameter is not needed it is not reported in the output. At the completion of each DOCK run, the number of molecules that were proc ...mation Search Tree), and a breakdown of the interaction energy between the ligand and receptor (see Scoring).

...GA). Maybe you are interested to find out if a bioactive conformation of a ligand as represented in a crystal structure is actually generated by OMEGA. ===1. Output OMEGA conformations (generated by dbgen.csh) into mol2 file===

...the PLOP control file to perform more sophisticated analysis. The scoring output format is consistent with that of [[MUD - Michael's Utilities for Docking]] Simply invoke <code>eplop</code> with paths to the receptor and the ligand:

...he docking procedure, ligands are read in from a single MOL2 or multi-MOL2 file. Atom and bond types are assigned using the DOCK 4 atom/bond typing paramet ...cored.mol2. Beyond this option, there are several other levels of sampling output:

...dentified with the chemical_match_file parameter and reside in an editable file (see chem_match.tbl). If a match will produce unfavorable interactions, the

This may take awhile but it will pull all your results into a single file, etc. If you want to calculate enrichment, etc.: $d37/enrich.py -l ligand-file -d decoy-file

This may take awhile but it will pull all your results into a single file, etc. If you want to calculate enrichment, etc.: $d37/enrich.py -l ligand-file -d decoy-file

...and atom and receptor atom can be calculated as the solvent affinity of a ligand atom weighted by the volume of the solvent displaced from the receptor atom ...affinity of Si and a fragmental volume of fi. The solvent affinity of the ligand atom is calculated as:

-v, --verbose lots of debugging output receptor input pdb file, (default: rec.pdb)

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

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

* 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

...>', 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

...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:

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

== 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

3) Add in your ~/.profile file : 2) Import ligands, and create ligand index file :

The output of both the script results and the log files are organized in a similar fas ...is submit-all-jobs.bash. This script takes in a source SMILES file and an output destination.

...ing a new directory is a good idea because these scripts generate a LOT of output files. ...r use a .smi file containing lines of smiles strings and ids or some other file type easily converted to smiles (i.e. multi .mol2 or .sdf). The optional PR

The script "charge_cofactor.csh" that takes as input a mol2 file with very strict mol2 naming. You will need to have Ligand pdb file ( LZ6.pdb ). This file should have hydrogen.

goes in your .cshrc/.login file (and you have to have python+numpy in your path) Then with a pdb file you run:

The '''first''' argument can be a multi-molecule MOL2 file. In this case, each entry will be compared to the molecule referenced by th ...he molecule(s) in the first file when compared against those in the second file.

# OUTPUT ...10.0 #number of seconds before quitting on any given ligand

Input for flexible docking requires a single PDB file with alternate atom positions (for every atom) for residues that you want t ...red against all possible combinations of receptors and written out, so the output files can be large (control during prospective screening with the save_limi

[[File:Piperidine opioid coords.png|thumb|upright=1.35|right|alt=Opioid ligands ex Sometimes it is interesting to search for a substructure in your DOCK output poses and calculate distances to a reference point. This is what filter.py

...al. J. Comp. Chem. 2004) for ligand molecules. The interaction between the ligand and the protein is represented by electrostatic and van der Waals energy te E(Complex) - [E(Receptor) + E(Ligand)],

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

What follows is a documented sample INDOCK file for [[DOCK 3.6]]. Many lines are required, lines starting with # are commen '''NOTE: do not under any circumstances use tab characters in this file.'''

These file are in the /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_wiki- ==Step 1. Custom Ligand and Library Generation ==

These file are in the /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_wiki- ==Step 1. Custom Ligand and Library Generation ==

These file are in the /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_wiki- ==Step 1. Custom Ligand and Library Generation ==

These file are in the /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_wiki- ==Step 1. Custom Ligand and Library Generation ==

[[File:workflow_FEP.png|thumb|center|550px]] * Begin by importing the structure of interest with a ligand that you are confident about. (FEP works best with an experimentally determ

[[File:DOCK3.7tuturial.2017.06.28.png|thumb|center|500px|Search for Your Molecule ...ase into the split database index file (this file usually contain many db2 file):

...o startdockbksX, but also indicates job submission by touching a submitted file in each directory. *Remove docking output leaving only input - will DELETE even completed jobs

* database file containing conformational expantion of your small molecules. =DOCK 3 INPUT FILE and Parameters=

INPUT FILE*: rec.ms #molecular surface file

Here we explain line by line the meaning of the header in the OUTDOCK 3.7 file. Solvation type: context-dependent ligand desolvation

...ion of specific atoms in the protein receptor to modify (enhance/decrease) ligand preferences for specific parts of the binding site. Generally one would red ...to trim down the electrostatics grid to the size of the van der Waals and ligand desolvation grids)

-o output_file #Output written to output_file, or grid.out if not specified -t Reduced output level

* A structure for your receptor protein provided as a pdb file 1) Supply ligand in binding site

...ese files is to run Trent's be_balsti wrapper on your PDB. If you have the file, 1YPE.pdb, in your current directory, run the following command: ...these, but double check that they are renamed to "CYX" in your rec.crg.pdb file after blastermaster runs.

It requires a SMILES file and the number of molecules you would like from each molecular weight/cLogP [[File:Minus2.png|thumb|center|500px|Choose the -2 charged tranches for your extre

You should visualize these sphere in UCSF Chimera to make sure that they file the site and do not go outside [[DOCK_3.7_2014/09/25_FXa_Tutorial#Receptor_ Alternatively, this command will find all ligands close to your the ligand.

** Download the tar.gz file and copy it to your desired location on the cluster. ** tar -zxvf [file name].tar.gz

=== making ligand databases. === bash $DOCKBASE/ligand/generate/build_smiles_ligand.sh ../actives_final.ism

Currently, the format of the mol2 file is very rigid. It must be in the same format as mol2s produced by ''DOCK 3 The following script will process a mol2 file produced by dock for rescoring.

...g the atoms, sorting to get the hit list, saving the hit list, and writing output. The way ligands are read in has also been re-written. • Northwestern DOCK accepts the name of an INDOCK file as argument on the command line. If no argument is provided, INDOCK is ass

# use the receptor and ligand the align to the MD frame. # modify the INDOCK file.

==Modifying the PDB file== *generate the file <tt>xtal-lig.pdb</tt> , which should only contain atoms of the molecular mo

In order to account for ligand desolvation and electrostatic interactions in the low-dielectric environmen Output files are stored in the generated ''pdb2gmx'' directory

* <code>empty.sh</code> which clears output files from previous runs (subdock needs the previous files cleared) ...yer" down the dependency tree. However, with the utility, we can run it to output a makefile dependency list to tell makefile in what order files must be com

The internal degrees of freedom of the ligand can be sampled First, the largest rigid substructure of the ligand (anchor)

create a python file called "0000.autodude_db_download.py" file = line.replace('"',' ').split()[2]

...ishlist for features that would be nice for a new version of the flexibase file format to support. mol2db2 format features that are actually implemented so *arbitrary information to be written into output mol2 file (5th and above M lines) [x]

create a python file called "0000.autodude_db_download.py" file = line.replace('"',' ').split()[2]

you can add the following to your environment file (.cshrc) for just issue them on the command line. * download 4NVE form the PDB brake it into receptor and ligand pieces.

you can add the following to your environment file (.cshrc) for just issue them on the command line. # This script runs beblasti, creates dirs and splits pdb into rec and lig file for running amber MD.