Operating systems: Windows, MacOS and Linux.

Contacts : João Ribeiro Nuno Sousa Cerqueira Pedro A. Fernandes Maria João Ramos

Citation :

CompASM: an Amber-VMD alanine scanning mutagenesis plug-in.
J. Ribeiro, N. M. F. S. A. Cerqueira, I. S. Moreira, P. A. Fernandes AND M. J. Ramos
Theoretical Chemistry Accounts, 2012, 131:1271
10.1007/s00214-012-1271-2

Protein-protein interactions play a crucial role in molecular recognition and cellular function. Mapping them, provides important insight on how these structures interact and on how to improve or inhibit their binding.

CompASM presents here as a very intuitive plug-in for two widely distributed softwares ( AMBER-Visual Molecular Dynamics (VMD)) that allows the user to perform a full Alanine Scanning Mutagenesis (ASM) procedure, requiring only very little user effort. This software is composed by two main packages: the Core and Graphical User Interface (GUI).

The CompASM Core section (Amber dependent, VMD independent) contains the main procedures of the ASM algorithm, e.g. Molecular Dynamics Simulation and MMPBSA calculation. It can be launched in a shell command and/or with the “Run” button of the GUI.

The CompASM GUI section (Amber independent, VMD dependent) turns possible the communication between Amber and VMD. Here, the user can generate the input file and submit it to the CompASM Core automatically, as well as being able to visualize the interfaces and the final results.

In order to run the compASM plug-in, the Visual Molecular dynamics software (VMD) must be installed. It can be found at http://www.ks.uiuc.edu/Research/vmd/ .

The compASM plug-in runs in any platform where VMD runs, i.e., Windows, OSX and LINUX.

1. Install the VMD software ( if you haven't yet installed).
2. Download the CompASM package.
3. Uncompress the tar.gz (or .zip) file to your Desktop folder
4. Run the installation program:

Unix OS- Open a shell window and type:

   cd
   cd Desktop/CompASM
   tclsh8.5 install.tcl
  

Windows- Double-click on the install.tcl file

1. Follow the instructions given in the window
2. Start VMD.
3. Edit amber_run.sh file to a proper sander launch (file containing the command to launch sander tool)