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compasm [2013/10/02 16:41] nuno [1. Introduction] |
compasm [2013/10/03 09:53] (current) nuno [2. ScreenShots] |
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//CompASM: an Amber-VMD alanine scanning mutagenesis plug-in.//\\ | //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 \\ | J. Ribeiro, N. M. F. S. A. Cerqueira, I. S. Moreira, P. A. Fernandes AND M. J. Ramos \\ | ||
- | Theoretical Chemistry Accounts, 2012, 131:1271 | + | Theoretical Chemistry Accounts, 2012, 131:1271\\ |
[[http://link.springer.com/article/10.1007%2Fs00214-012-1271-2|10.1007/s00214-012-1271-2]]\\ | [[http://link.springer.com/article/10.1007%2Fs00214-012-1271-2|10.1007/s00214-012-1271-2]]\\ | ||
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===== 2. ScreenShots ===== | ===== 2. ScreenShots ===== | ||
- | {{gallery>software:compasm:screenshots?*&150x150&lightbox}} | + | {{gallery>software::compasm?*&150x150&lightbox}} |
===== 3. Download ===== | ===== 3. Download ===== | ||
- | In order to run the **//volArea//** plug-in, the Visual Molecular dynamics software (VMD) must be installed. It can be found at http://www.ks.uiuc.edu/Research/vmd/ . | + | 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/ . |
<note tip> | <note tip> | ||
- | * VolArea Plug-in : **v1.0** {{:download-big.png?direct&100|}} | + | * compASM Plug-in : **v1.0** {{:download-big.png?direct&100|}} |
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- Install the VMD software ( if you haven't yet installed). | - Install the VMD software ( if you haven't yet installed). | ||
- | - Extract vmdMagazine.zip file to a directory in the disk. | + | - Download the CompASM package. |
- | - Once unpacked, we need to let VMD know of this location. To do so, edit your VMD start-up file and add the biopathfinder plugin directory to the auto_path variable (see below). | + | - Uncompress the tar.gz (or .zip) file to your Desktop folder |
- | - Once this procedure is complete the BioPathFinder plugin can be found at the VMD extensions menu (CompBioComp>>vmdMagazine). | + | - 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 | ||
+ | |||
+ | |||
+ | - Follow the instructions given in the window | ||
+ | - Start VMD. | ||
+ | - Edit amber_run.sh file to a proper sander launch (file containing the command to launch sander tool) |