Difference between revisions of "Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)"
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Example input for both A9OPTIM and COPTIM has been uploaded [http://www-wales.ch.cam.ac.uk/examples/OPTIM/normalmodes/ here]. These archives contain all you need to run OPTIM in this way, and the input is commented to make it easy to adapt to other molecules and situations. If you have problems running this input, and are sure OPTIM has been compiled correctly, ask someone for help! :) |
Example input for both A9OPTIM and COPTIM has been uploaded [http://www-wales.ch.cam.ac.uk/examples/OPTIM/normalmodes/ here]. These archives contain all you need to run OPTIM in this way, and the input is commented to make it easy to adapt to other molecules and situations. If you have problems running this input, and are sure OPTIM has been compiled correctly, ask someone for help! :) |
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| − | Visualising the data produced is covered in a separate example archive and tutorial located [[Visualising output of an OPTIM normal mode analysis here]] |
+ | Visualising the data produced is covered in a separate example archive and tutorial located [[Visualising output of an OPTIM normal mode analysis | here]] |
Revision as of 11:49, 2 April 2009
OPTIM is able to perform harmonic normal mode analysis on stationary points.
Example input for both A9OPTIM and COPTIM has been uploaded here. These archives contain all you need to run OPTIM in this way, and the input is commented to make it easy to adapt to other molecules and situations. If you have problems running this input, and are sure OPTIM has been compiled correctly, ask someone for help! :)
Visualising the data produced is covered in a separate example archive and tutorial located here