When you load your trajectory in VMD, go to Analysis and then TK Console. Ott-sasa.txt: Tcl script for analyzing surface area of a polar oil droplet. One can either append the following command in C:autoexec.bat and execute it. Oct-sasa.txt: Tcl script for analyzing surface area of a non-polar oil droplet. if you want a more automated way, then you need to know the exact atom name and the residue number. where x is the index of the atom of an residue in which you are interested. 0.14 nm) to measure the surface area of a selected region(s).Ĭourtesy of Keith Callenberg from Wikipedia ![]() o: gromacs trajectory file (six frames) of a polar oil cluster (30 octanethiols) interaction with a kerogen surface Example 2: calculate the surface area (SA) of oil droplet Solvent-accessible surface area method uses a imaginative sphere with a given probe radius (e.g. Ott-count.txt: Tcl script for counting numbers of polar oil atoms (resname OTT) within 3.6 Angstroms of kerogen surface This guide documents the usage of both the graphical user interface and the text console interface for displaying and grapically manipulating molecules. Oct-count.txt: Tcl script for counting numbers of non-polar oil atoms (resname OCT) within 3.6 Angstroms of kerogen surface (resname KER) This documentation includes user guide for opening and loading molecular structure files, change drawing options of molecular structures like CPK, tube, ribbon and etc., change color styles of. Type "source ott-count.txt" to execute the script and the data will be saved as "count_out.txt".This will load the procedure defined in distance.tclinto the VMD. 3 In the the TkConsole window, load the script into VMD by typing: source distance.tcl(make sure that the file distance.tclis in the current folder). " to navigate and "pwd" to show current directory) Open the TkConsole window by selecting Extensions Tk Consolein the VMD Main menu. ![]() ![]()
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