Download
Below are the binaries (Fortran77) for the fast computation of binding and contact free energies. Download the binary for your system.
- fastcontact.x (Linux)
- fastcontactibm.x (IBM SP)
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
- charmm19.rtf ("RTF file")
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):
- corn18.dat ("atomic contact potential matrix file")
Usage
Syntax:
fastcontact.x RTF rec.pdb lig.pdb Num_extra_ligands Contacts SASA [< extra_ligand_list] [> stdout]
where
- RTF is a file that defines the united atom composition of each amino acid (provided together with the binary);
- Num_extra_ligands is a file with the names of new ligand structures;
- If Contacts != 1, the output details the top 20 residues that have the minimum and maximum contribution to the different free energy components; the residues are renumbered starting with number 1 and the program creates two PDB files with the new numbers. If Contacts = 1, no contact energy information is produced; and
- Solvent accessible surface area (SASA); SASA != 1 will check that at least one of the contact residues is at the surface. If this constraint is not deemed necessary, then set SASA = 1
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:
- rec.pdb ("receptor")
- lig.pdb ("ligand")
- b1.pdb ("extra ligand #1")
- d3.pdb ("extra ligand #2")
- ligand1.pdb ("extra ligand #3")
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)