MDcons(Molecular Dynamics consensus) Code
Interpretation of Biomolecular MD simulations
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S. Abdel-Azeim, E. Chermak, A. Vangone, R. Oliva & L. Cavallo,
BMC Supplement for BITS 2013
KAUST - University of Napoli "Parthenope"
website : https://www.molnac.unisa.it/BioTools/mdcons/index.php
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======== Informations ==========
MDcons allows to characterize the molecular dynamics of the interface
in Protein, RNA, DNA and ligand complexes. It is a complementary tool for the
analysis of MD simulations of both experimental and predicted structures
of Protein, RNA, DNA and ligand complexes.
MDcons consists of a collection of fortran code with python
<http://www.python.org> and bash scripts. We have been running MDcons
without problems on Linux and MacOSX systems. Note that MDcons is
not currently supported on Windows systems.
You can run MDcons either for a collection of single pdb files or
a MD trajectory (e.g from GROMACS).
======== How to run MDcons ==========
Just launch MDcons by typing after installation :
launch_mdcons.sh
Your input may be of two types :
1) single trajectory pdb file without chain identifyer
2) set of snapshot pdb files with chain identifyer (in standard pdb format)
In case 1), you will be prompted to give the ATOM number where the second chain begins.
In case 2), you will be prompted to give the two chain names
====== Outputs generated =======
consensus_map.png png picture of the consensus map which represents the
frequency of inter-residue contacts for all the
MD simulation
consensus_tableALL.txt text file reporting a list of the inter-residue
contacts with relative conservation rates during
the MD simulations;
conservation_score.txt text file with the C50, C70 and C90 coefficient,
which represent the number of inter-residue contacts
conserved for at least 50, 70 and 90% of the analyzed frames
======== Example =========
To run an example job:
- copy the scripts from scripts/ and the executable of mdcons to the example/ folder.
- untar the trajectory example:
tar -xvjf example_200Frames.tar.bz2
launch_mdcons.sh
type "1"
type "y"
type "1373"
You should find the same results than the ones on the reference/ folder.
The 2nd chain of this protein-protein complex example starts from the
residue number 88 located at the ATOM number 1373.
===== How to cite MDcons =====
S. Abdel-Azeim, E. Chermak, A. Vangone, R. Oliva & L. Cavallo,
BMC Supplement for BITS 2013
======== Contact =========
oliva@uniparthenope.it, edrisse.chermak@kaust.edu.sa
======== Bugs =========
Please report any bug to : edrisse.chermak@kaust.edu.sa
======== FAQ =========
* Which type of input can MDcons handle ?
All files in standard pdb format, either Protein, DNA, RNA or Ligand. It is also compatible with GROMACS trajectories without chain identifyer.
* How can MDcons help me in my research ?
MDcons can provide additional informations to the RMSD evolution during the MD simulation, since it quantifies and provides a list and a map of the most conserved contacts occuring during the MD.
* How much time does it take to run Mdcons ?
MDcons runs 2000+ pdb files in less than 5 minutes on Intel Xeon processor with 4Gb of RAM machine.
* Where can I get a version of MDcons, is MDcons free of charge ?
You can download it on SourceForge at: \url{http://sourceforge.net/projects/mdcons/files/latest/download}. MDcons is under GPL license and free of charge. You can even have access to the source code, but if you modify it you have to publish it also under GPL.
