Go Replicants!

A molecular simulator of Go-type potentials

Latest version: 20110622

Author: Juan M. Bello Rivas

Scientific advisors: Benjamin Ivorra, Ángel M. Ramos, and Antonio Rey

Acknowledgments

This work is supported by the Spanish Ministry of Education and Science under project MTM2008-04621/MTM; the research group MOMAT (Ref. 910480) supported by Banco Santander and Universidad Complutense de Madrid; and the Comunidad de Madrid under QUIMAPRES project S2009/PPQ-1551.

Overview

Go Replicants! is a molecular simulator for proteins. It uses a replica exchange Monte Carlo strategy to explore the energy surfaces of Go-type potentials following the methodology explained in Thermodynamics of Go-type models for protein folding. Prieto L., de Sancho D., Rey A. The Journal of chemical physics. (2005) October; 123:154903.

This software is currently in alpha stage. Use at your own risk.

License

This software is released under the GNU General Public License. See the accompanying LICENSE file for details.

Prerequisites

The program has been tested on GNU/Linux platforms. A recent version of the GNU Scientific Library (1.14 or above) is required. It is also recommended to have ATLAS and Gnuplot installed.


Results at different temperatures

Usage

Building from source code

  1. Download the package from http://curio.mat.ucm.es/~jmbr/go-replicants/go-replicants-latest.tar.gz
  2. Extract the source code with tar xvzf go-replicants-latest.tar.gz
  3. cd go-replicants && mkdir build && cd build
  4. cmake -L ../devel && make

This builds the binaries molecular-viewer and molecular-simulator.

Running a simulation

You need the structural data of a protein in XYZ format for molecular-simulator to operate. Structural data downloaded in PDB format from the Protein Data Bank can be converted to XYZ format using a conversion script included in the scripts directory. To do the conversion write:

../pdb2xyz PROTEIN.pdb > PROTEIN.xyz

Once the structural data is in the right format one can run a simulation by executing

./molecular-simulator -d D -a A -t T1 -t T2 ... -t TN PROTEIN.xyz

In the previous command D and A stand respectively for the dmax and a parameters of the potential energy function and T1, ... , TN are the temperatures to be simulated (in dimensionless units). This produces two kinds of files with extensions .dat and .xyz. The former contain values of the potential energy function as the simulation proceeds and the latter contain the corresponding spatial conformations of the protein.

Bug reports

Please send bug reports and/or patches to the author's email address.