UserWiki:Meisam: Difference between revisions

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== FAQ ==

*What do I do here?

*:I calculate the stable geometry of the molecules with [https://en.wikipedia.org/wiki/Austin_Model_1 AM1]<ref>Austin Model 1</ref> semiempirical method, and [https://en.wikipedia.org/wiki/Hybrid_functional#B3LYP B3LYP]<ref>Becke, 3-parameter, Lee-Yang-Parr</ref> [https://en.wikipedia.org/wiki/Density_functional_theory density functional approximation] and upload my results here. These geometries can be used for ~~testing~~ in ligand binding to receptors or finding molecular characteristics such as IR absorption frequencies, etc.

*:I calculate the stable geometry of the molecules with [https://en.wikipedia.org/wiki/Austin_Model_1 AM1]<ref>Austin Model 1</ref> semiempirical method, and [https://en.wikipedia.org/wiki/Hybrid_functional#B3LYP B3LYP]<ref>Becke, 3-parameter, Lee-Yang-Parr</ref> [https://en.wikipedia.org/wiki/Density_functional_theory density functional approximation] and upload my results here. These geometries can be used for [https://en.wikipedia.org/wiki/Docking_(molecular) docking] tests in ligand binding to receptors or finding molecular characteristics such as IR absorption frequencies, etc.

*How '''accurate''' are these results?

*:It is hard to say. Although AM1 method considers only the valence electrons, but its results are fairly good. B3LYP results are much more accurate but they need comparatively huge amount of computation time. A simple geometry search which takes ~1 min using AM1, will take ~50-100 hours using B3LYP method on the same machine.

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 == FAQ ==
 *What do I do here?
-*:I calculate the stable geometry of the molecules with [https://en.wikipedia.org/wiki/Austin_Model_1 AM1]<ref>Austin Model 1</ref> semiempirical method, and [https://en.wikipedia.org/wiki/Hybrid_functional#B3LYP B3LYP]<ref>Becke, 3-parameter, Lee-Yang-Parr</ref> [https://en.wikipedia.org/wiki/Density_functional_theory density functional approximation] and upload my results here. These geometries can be used for testing in ligand binding to receptors or finding molecular characteristics such as IR absorption frequencies, etc.
+*:I calculate the stable geometry of the molecules with [https://en.wikipedia.org/wiki/Austin_Model_1 AM1]<ref>Austin Model 1</ref> semiempirical method, and [https://en.wikipedia.org/wiki/Hybrid_functional#B3LYP B3LYP]<ref>Becke, 3-parameter, Lee-Yang-Parr</ref> [https://en.wikipedia.org/wiki/Density_functional_theory density functional approximation] and upload my results here. These geometries can be used for [https://en.wikipedia.org/wiki/Docking_(molecular) docking] tests in ligand binding to receptors or finding molecular characteristics such as IR absorption frequencies, etc.
 *How '''accurate''' are these results?
 *:It is hard to say. Although AM1 method considers only the valence electrons, but its results are fairly good. B3LYP results are much more accurate but they need comparatively huge amount of computation time. A simple geometry search which takes ~1 min using AM1, will take ~50-100 hours using B3LYP method on the same machine.