Search results

...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)],