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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]