compasm
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This shows you the differences between two versions of the page.
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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]]\\ | ||
| Line 40: | Line 40: | ||
| ===== 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 | ||
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| + | |||
| + | Windows- Double-click on the install.tcl file | ||
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| + | |||
| + | - 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) | ||
compasm.1380728484.txt.gz · Last modified: 2013/10/02 16:41 by nuno
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