Go Replicants!
A molecular simulator of Go-type potentials
1 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.
Results at different temperatures
2 Prerequisites
You need a recent version (1.14 or above) of the GNU Scientific Library.
It is also recommended to have ATLAS and Gnuplot installed.
3 License
This software is released under the GNU General Public License. See the
accompanying LICENSE file for details.
4 Usage
4.1 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.
4.2 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.
5 Bug reports
Please send bug reports and/or patches to the author's email address.
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