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TinkerTools / tinker

Tinker: Software Tools for Molecular Design
https://dasher.wustl.edu/tinker/
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Query regarding use of poledit #147

Closed heman3333 closed 8 months ago

heman3333 commented 8 months ago

I am doing parameterization of a molecule. So in the process, we have to choose polarization groups within the molecule while using 'poledit' command over gdmaout file. What would be the specific command to do that, say, for Urea molecule ?

jayponder commented 8 months ago

POLEDIT has the user select from three options for setting polarization groups: (1) put all atoms into one group, (2) separate into groups at rotatable bonds, or (3) manual entry of the bonds that separate the molecule into groups.

For most cases, we recommend option (2), in which case POLEDIT will automatically separate the groups at bonds that freely rotate or at least rotate with low barriers at typical temperatures. This is the option we generally use for the AMOEBA or HIPPO force fields. For small organics, you can just use option (1) and put all atoms into a single polarization group. We do not suggest option (3) unless you have some specific reason for wanting to choose your own custom groups. Fortunately, in most cases, the choice of where to split the polarization groups should not have a big effect on the performance or results from the model.

heman3333 commented 8 months ago

Thank you very much for the clarification.