McVol

Calculating the Volume of Proteins and finding internal cavities.

This program was developed to integrate the molecular volume, solven accessible volume an Van der Waals volume of proteins using a Monte carlo algorithm. Based on this calculations, McVol is also able to identify internal cavities as well as surface clefts und fill these cavities with water molecules. Additionally, a membrane of dummy atoms can be placed as a disc atound the protein. The program is available under the Gnu Public Licence. A precompiled binary (X86) can be downloaded free of charge from here.

1. Download the file
2. type tar -jxf McVol.tar
3. Go to the directory McVol/test: cd McVol/test
4. Type ../src/McVol all

The programm will run for about 1 minute. In the result you will see the cavities identified in bacteriorhodopsin, the volume of these cavities and the number of water molecules placed in each cavity. In the cav directory, you will find a dot representation of the cavities and clefts. You will also find the a membrane of dummy atoms. You can visually inspect all of these by loading all.pqr, cavity*, real_cleft* and memb.pqr in your preferred molecule browser.