Use Tinker

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Use Tinker
Computational Chemistry 5510 Spring 2006 Hai Lin
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Introduction to Tinker
http//dasher.wustl.edu/tinker/ A complete and
general package for molecular mechanics and
dynamics, with some special features for
biopolymers Use of many common force field
parameter sets, such as Amber, CHARMM, MM2 and
MM3, OPLS, and AMOEBA Available for most of the
platforms (Unix, Linux, Mac, and Windows) A
graphic interface for visulaization and input
setup (Linux, Mac, and Windows)
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Files Used by Tinker

• Input
• Coordinate file .xyz
• Parameter file .prm
• Keyword file .key
• Executable/Binary
• Analyze, Newton, Testgradient ...
• Output (on monitor or saved to a file)
• Cordinate file .xyz_2, ...
• Output file .log

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Example of Coordinate File
Total of atoms
Connectivity (atoms that it bonded to)
Comments
X, Y, and Z coordinates (Å)
14 C4H10 //charmm27 1 CT3 -1.85185185
0.95959595 0.00000000 27 2 3 4 5 2 HA
-1.49517901 1.46399414 0.87365150 1 1
3 HA -1.49517901 1.46399414 -0.87365150
1 1 4 HA -2.92185185 0.95960913
0.00000000 1 1 5 CT2 -1.33853613
-0.49233621 0.00000000 26 1 6 7 8 6
HA -1.69520716 -0.99673375 0.87365262 1
5 7 HA -1.69521086 -0.99673560
-0.87365004 1 5 8 CT2 0.20146387
-0.49235441 -0.00000377 26 5 9 10 11 9 HA
0.55813402 0.01034635 -0.87463418 1 8
10 HA 0.55813884 0.01374031 0.87266518
1 8 11 CT3 0.71477959 -1.94428382
0.00281556 27 8 12 13 14 12 HA 0.35773857
-2.45050723 -0.86962904 1 11 13 HA
1.78477949 -1.94429737 0.00236500 1 11 14
HA 0.35847495 -2.44685455 0.87766964 1
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Atom index
Atom type
Atom type index
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Graphic Interface

• Graphics
• Visulaize the moleculars.
• Model Commands
• What kinds of computations (single-point energy,
  geometry optimization, molecular dynamics, etc.)
  to be performed?
• Keyword Editor
• Set options for calcuations and output (unit of
  energy, temperature for simulation, etc.)
• Logs
• Look at what we get.

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Example Calculation Butane

• Preparation
• Tinker is installed at C\Program files\Tinker.
• Examples are under the example and the test
  subdirectories.
• Make your own subdirectory (e.g., hailin)
• Copy butane.xyz from the test subdirectory to
  your own subdirectory.
• Calculation
• Run Tinker and Open butane.xyz from your
  subdirectory.
• Selecet MM3 force field parameters.
• Go to Modeling Commands, select Analyze, and
  check E (total energy), D (details), and P
  (parameters).
• Launch the job.

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Example Calculation Butane (2)

• Results
• Go to the Logs, and view the output.
• Check the individual energy contributions.
• Check the summary of the total energy.
• Check the parameters for each individual term.
• Clean-up
• Go to your own subdirectory.
• Delete files that you no longer need, e.g.,
  butane.log.

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Your Homework

• Practise with Tinker
• Calculate the single-point energy for two example
  systems in the Tinker distribution.
• Suggested systems
• Alanine dipeptide (three conformations c5, c7a,
  and c7e) using the charmm27 force field. You can
  compare the energies for these three
  conformations.
• Heme group with Iron (heme) using the charmm27
  force field.