View source for Mod:gv advanced

'''Advanced GaussView Building Tutorial'''

''There are several useful options available in GaussView to help build and manipulate large molecules. In these tutorials, we cover some of the less standard options available in the package''.

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== Appending a structure ==


Combining two structures together that have been built and/or optimized separately can be useful for building dimers or docking substrates into proteins.

[http://www.gaussian.com/g_tech/gv5ref/tut0.htm#4 Click here] for the tutorial on Building Tyrian Purple Dye as an example of how to append a structure.

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== Creating a custom fragment==

You can build your own fragment in GaussView and save it to the '''Custom Fragment Library''' which can save time if your molecule has several bulky ligands that have the same structure.

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(1) Build the Si(CH<sub>3</sub>)<sub>3</sub> fragment.

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(2) Add the created fragment to the Custom Fragment Library by following the instructions given here: [http://www.gaussian.com/g_tech/gv5ref/advbld.htm Custom Fragment Library].

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(3) Build the following radical using the custom fragment created in (2) and save the structure to a file.

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[[Image:P(CH(Si(CH3)3)2.jpg]]

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(4) Optimize the radical using '''PM3'''. You are advised <u>NOT</u> to use the '''Clean''' function first in this case as it tends to result in overlapping methyl groups.

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(5) The above radical dimerises. Open the same radical again in the same window by selecting '''Append all files to active molecule''' when you open the output file generated in (4). Now build the dimer. See if you can optimize it at the '''PM3''' level also.

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== Editing files in GaussView ==


There are limitations in GaussView for setting up certain Gaussian jobs. An example of this is when one would like to change the isotope of an atom in a frequency calculation. Here we look at the effect of substituting D for H in methane.

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(1) Draw a methane molecule and set up an optimization and frequency calculation at the '''HF/3-21G''' level. Run the calculation and visualize the vibrational frequencies.

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(2) Starting from the optimized structure, set up a new frequency calculation at the same level of theory. Add the keyword '''Freq=ReadIsotopes''' in the '''Additional Keywords''' field. Click '''Update'''.

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(3) We will set up a frequency calculation at a different temperature (200K) and at 1 atmospheric pressure, replacing one of the hydrogen atoms with deuterium. Click on the '''Edit''' button. You will be prompted to save the file. The input file will then be opened in WordPad.

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(4) Now edit the input file manually to add the temperature, atmospheric pressure and isotopes as shown below (comments are in <font color="#FF0000">'''red'''</font>). These should be listed at the end of the input file after the molecule specification separated by a blank line. Remember to leave a blank line at the end of the input file.

 <nowiki>
 %mem=256Mb
 %chk=DCH3.chk
 %nproc=1
 #p HF/3-21G Freq=ReadIsotopes
 
 DCH3
 
 0 1
  C
  H                  1              B1
  H                  1              B2    2              A1
  H                  1              B3    3              A2    2              D1
  H                  1              B4    3              A3    2              D2
 
    B1             1.07000000
    B2             1.07000000
    B3             1.07000000
    B4             1.07000000
    A1           109.47120255
    A2           109.47125080
    A3           109.47121829
    D1          -119.99998525
    D2           120.00000060
 </nowiki><font color="#ff0000">''' '''blank line</font >
 350.0 1.0 <font color="#ff0000">temp pressure [scale]</font >
 12.0 <font color="#ff0000">isotope mass for atom 1</font>
 1.0 <font color="#ff0000">isotope mass for atom 2</font >
 1.0 <font color="#ff0000">isotope mass for atom 3</font >
 1.0 <font color="#ff0000">isotope mass for atom 4</font >
 2.0 <font color="#ff0000">isotope mass for atom 5</font >
 ''' ''' <font color="#ff0000">blank line</font >
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(5) Go to '''File''' and select '''Save'''. Close the Word Pad file. You will now be asked if you want to submit the job. Click '''OK'''.

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(6) Once the job has finished, visualize the vibrational frequency and see how they have changed.

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== Manually editing files outside GaussView ==


You can edit the input files manually without using GaussView, either by opening the files in Word Pad or in '''Gaussian09W'''. Jobs can then be submitted directly using '''Gaussian09W'''.

Further information about Gaussian can be found at the Gaussian web site http://www.gaussian.com