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--- madamm [2013/10/02 15:46]
nuno [4. Installation]
+++ madamm [2013/10/03 09:56] (current)
nuno [2. ScreenShots]
@@ Line 4: / Line 4: @@
 //Operating systems: MacOS and Linux.//
-{{:b-download.png?direct&100|}}
+[[http://www.fc.up.pt/pessoas/nscerque/download/MADAMM.tar.gz|{{:b-download.png?direct&100|}}]]
 Contacts : [[nscerque@fc.up.pt|Nuno Sousa Cerqueira]] [[pafernan@fc.up.pt|Pedro A. Fernandes]]  [[mjramos@fc.up.pt|Maria João Ramos]]
@@ Line 11: / Line 11: @@
 <WRAP column 15%>
-{{:quantumchemcirty.gif?direct&100|}}
+{{:madammcover.gif?direct&200|}}
 </WRAP>
-**__Citation :__** \\
+**__Citation :__**
+//MADAMM: a multistaged docking with an automated molecular modeling protocol.//\\
+N. M. F. S. A. Cerqueira, N. F. Bras, P. A. Fernandes AND M. J. Ramos\\
+Proteins (Structure, Function, Bioinformatics), 2009, 74(1):192–206
+[[http://onlinelibrary.wiley.com/doi/10.1002/prot.22146/full|DOI:10.1002/prot.22146]]
-//VsLab—An implementation for virtual high-throughput screening using AutoDock and VMD.//\\
-N. M. F. S. A. Cerqueira, J. Ribeiro, P. A. Fernandes AND M. J. Ramos \\
-International Journal of Quantum Chemistry, 2011, 111(6):1208–1212
-[[http://onlinelibrary.wiley.com/doi/10.1002/qua.22738/full|DOI:10.1002/qua.22738]]\\
 ----
 ===== 1. Introduction =====
@@ Line 45: / Line 51: @@
 <note tip>
-  * VsLab Plug-in  : **v1.0** {{:b-download.png?direct&100|}}
+  * MADAMM   : **v1.0** [[http://www.fc.up.pt/pessoas/nscerque/download/MADAMM.tar.gz|{{:b-download.png?direct&100|}}]]
 </note>
 ===== 4. Installation =====
 ###
-VsLab can only be installed in LINUX and MAC operating systems, due to the limitations of the GOLD and Charmm software.
+MADAMM can only be installed in LINUX and MAC operating systems, due to the limitations of the GOLD and Charmm software.
+###
 To install MADAMM just download the zip file and extract it using the following command:
@@ Line 65: / Line 69: @@
     ./MADAMM.sh
-In order to run MADAMM software you also need to install dependencies. Please go to Install Dependencies for more information.
+==== 4.1. System Dependencies ====
+###
+MADAMM supports computers running MacOS-X, Unix, or Windows, and is distributed free of charge. However at the moment it is advisable to run MADAMM in LINUX systems.
+In order to use MADAMM you need to install in your computer the following software:
 ###
-==== 4.1. System Dependencies ====
+  * **tcl/tk**
-Two programs must be installed in order to run vsLab:
+###
+In most of the LINUX distributions tcl/tk is already installed in the system. You can check it writing tclsh in your terminal. Even so, it is recommended the installation of the activestate tcl/tk that already comes with the modules that are necessary to run MADAMM. You can download it from http://www.activestate.com/ (Just follow the direction : download>language distributions>activetcl).
+###
+To install active state you just have to write in the terminal:
-  - The program VMD (http://www.ks.uiuc.edu/Research/vmd )
+    tar -xvzf ActiveTcl8.4.14.0.272572-linux-ix86.tar.gz
-  - The sqlite database engine (http://www.sqlite.org)
+    cd ActiveTcl8.4.14.0.272572-linux-ix86/
-  - AutoDock Suite (http://autodock.scripps.edu)
+    ./install.sh    (note : you must have root permissions for this command)
+  * **VMD**
 ###
-The first program can be easily installed with the tutorials available in the VMD  site ( version 1.8.7 is required).
+MADAMM has a small interface that allows to analyse all the results using VMD.
+VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. You can get VMD from http://www.ks.uiuc.edu/Research/vmd/.
 ###
+  * **gnuPLOT**
 ###
-The sqlite database engine is generally installed in all UNIX/LINUX systems (to see if it is installed just write in the terminal: sqlite) If it is not installed you can install writing the following commands in the terminal under the root privileges:
+MADAMM has a small interface that allows to plot severall results in different formats using gnuPlot.
+gnuPlot is a portable command-line driven interactive data and function plotting utility.You can get gnuPlot from: http://www.gnuplot.info/
 ###
-   Ubuntu OS : sudo apt-get install sqlite
-   fedora OS : yum install sqlite
-   Mac       : (see user manual)
+  * **GOLD and CHARMm**
 ###
-VsLab also depends on autodock and autogrid executables. Therefore they  must be installed in the systems before  the installation of vLab proceeds.
+You need these proprietary software to run the docking software and the molecular mechanics forcefield that are the required by MADAMM.
 ###
-The installation of AutoDockTools program is also required.
-==== 4.2. Install VsLab ====
-Only three steps are required to run VsLab:
-  * Unordered List ItemExtract the file vsLab.tar.gz to a directory of your choice.
-   tar -xvzf vsLab.tar.gz
-  * Run the program install.tcl and follow the instructions:
-   cd vsLab
-   tclsh install.tcl
-Then the user just have to follow the guidelines that are provided by the script.
 ###
-After the installation ends you can find vsLab inside VMD application, at the plug-in the menu: Extensions» PortoBioComp»virtal screening Lab
+At the moment the program can only use these two programs but in future releases it will be possible to use also AutoDock and GROMACS and AMBER as molecular mechanic force fields.
 ###
-===== 5. Tutorial =====
-not available yet.
 ----

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