Search results

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)],

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