A shell script for automized processing of pdb-files with vmd http://www.ks.uiuc.edu/Research/vmd/ and APBS http://www.ks.uiuc.edu/Research/vmd/plugins/apbsrun/.
- pdb files are converted to pqr-files.
- the electrostatics are calculated (with VMD, using the amber force-field)
- exports as wavefront-obj-files and as dx-files the electrostatic potential
- creates one big picture containing the es,el,ss pictures of all the input molecules
- creates a gif containing all el -pictures
Copy the Folder /ExampleHierarchy/ to your desired location. Rename the folder as you wish. Copy your pdb-files into /ExampleHierarchy/Input/pdb/
After setting up the folder hierarchy omit the following call from the folder containing Input and Output
<pathToMutComp>./process.sh
where pathToMutComp is the path to the local repository on your machine.
An example is included in M43Copy. To run the example with you can do:
cd /M43Copy
.././process.sh
the results will be stored in /M43Copy/Output.
In order to use the graphical-user-interface go to /GUI/build-GUI-Desktop-Debug/ and click on the executable GUI.
parametersFile pecifies the path to where the parametersFile parameters.txt can be found.
If you want to have your pictures appear in a specific ordering add a file ordering.txt in the output-folder. This file has to contain the names of the proteins in the order that you want them to apper in the file overview.png.
Willy Bruhn, MD Faruq Hossain