Download

Below are the binaries (Fortran77) for the fast computation of binding and contact free energies. Download the binary for your system.

Dependencies: Make sure you have libf2c installed on your machine.

Note: You must set the appropriate permissions for running these binaries (e.g. "chmod +x fastcontact.x").

You will also need the definition of the atomic composition of each amino acid (the "RTF file"). This RTF file is consistent with CHARMM19 parameters.

Note: Proteins should have polar hydrogens to obtain meaningful electrostatic interactions

The following atomic contact potential matrix file ("corn18.dat") is given as a reference, it is not needed to run FastContact (From Zhang C, Vasmatzis G, Cornette J, DeLisi C (1997). JMB, 267:707-726):

Usage

Syntax:

fastcontact.x RTF rec.pdb lig.pdb Num_extra_ligands Contacts SASA [< extra_ligand_list] [> stdout]

where

Example 1

Download the following files:

Then execute the following command:

./fastcontact.x charmm19.rtf rec.pdb lig.pdb 0 0 0 > output1.txt

The results from the above run are found in the file "output1.txt". They should be identical to the results found in this file: contact_energies1.txt.

Example 2

In order to screen several ligands simultaneously, it is necessary to add an optional argument at the end of the command string.

Download the following files:

Create a text file (lets call it "extra_lig_list.txt") containing a list of the filenames of the extra ligands (one filename per line) as follows:

b1.pdb
d3.pdb
ligand1.pdb

Then execute the following command:

./fastcontact.x charmm19.rtf rec.pdb lig.pdb 3 1 0 < extra_lig_list.txt > output2.txt

Note: For Num_extra_ligands > 0, you must pipe in a list file (i.e. "< extra_lig_list.txt").

The results from the above run are found in the file "output2.txt". They should be identical to the results found in this file: contact_energies2.txt

Please cite: Bioinformatics 2005 (e-published; see below)


last update: 22-Mar-2007