A Use a script to extract coordinates and energies from these files and store

A use a script to extract coordinates and energies

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A. Use a script to extract coordinates and energies from these files and store them in an .xmol file. There are two scripts that will be useful (get them from Paul): ircextract.awk and ircextract2.awk. The second is to be used when you have edited gaussian's z-matrix. The syntax is as follows: awk -f ircextract2.awk h0005a1.out >h0005a1.xmol This takes the data from the output file and stores just what you need in an xmol file. Note: to look at the unoptimized geometries Polo created another script to do the same thing--it is optextract.awk It may be useful to use this script to look at the unoptimized structures when the irc calc is going awry. B. Then use WordPad to create individual .txt files (step #, energy, coordinates). It may be easier to store these files in the PDB folder of the PyMOL folder for later use, but this is not crucial. Open two windows and copy each step into a new .txt file. In this case I took data from the .xmol file and made files h0005a1.txt to h0005a10.txt In future I recommend use of f and r for the forward and reverse IRC calc., e.g. h0007f.out, h0007r.out. The .xmol files would have the same name, and then, the .txt files could be named h0007f1.txt, h0007f2.txt etc. C. Manually change suffix of all these files to .xyz. This can be done beautifully if you know DOS and use the Command Prompt ls is now dir, cd is the same, what you can do is to go to the command prompt (programs -> accessories -> command prompt) You need to go to the directory of where the files are located, then use the
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Carlier Group Gaussian User Manual 50 rename command, in this case: rename h*.xyz h*.txt I have been looking for good renaming programs for Mac. So far I have tried Skooby Renamer and R-Name . Still learning these. D. Use gOpenMol to import the XYZ files, and export .pdb files. This is done using Import and Export commands, obviously. PyMOL can only read pdb files, that is why we are doing this. Now go to the "Using PyMOL to make movies" Section 18. below. Can we find another way to go from .xyz to .pdb? Will Molden work? Will newzmat work? Should we write an .awk script? 18. Using PyMOL to Make Movies A. Use PyMOL to load all the .pdb files ( PyMOL can't read .xyz). This is done at the command line, specifying the path load pdb\h0005a1\h0005a1.pdb Load the reverse IRC structures in reverse order Load the TS structure Load the forward IRC structures in forward order Once you've loaded them all, use 'Save Session As' to save the collection of molecules for future use. Once all of them are loaded, you can turn individual ones off by clicking the button, or type 'disable all' to turn them all off B. Reorient selected structures, if necessary Sometimes the coordinate system appears to have changed and the molecules don't overlay correctly. You can then select the first structure and the second structure. Go to Wizard/Pair Fitting and then use CNTRL-Middle Click to select atom pairs--in each case select the one you want to move, and then the one you want to move it to. Select three pairs in all, and then click the 'Fit 3 pairs' button. If it looks good, click done.
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  • Fall '19
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