Talk:Logs:parameterization
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The list of Molecular Functional Groups used:
- acid
- alcohol
- aldehyde
- alkane
- alkene
- alkyl bromide (alkane w/ Br)
- alkyl chloride (alkane w/ Cl)
- alkyl iodide (alkane w/ I)
- alkyne
- amide (-NC=O)
- amine （N w/ 1 lone pair)
- arene
- aromatic compound
- aryl chloride
- carbonitrile (-C#N)
- carboxylic acid
- cyclic hydrocarbon
- ester (R -C(=O)O- R')
- ether (R -O- R')
- halogen derivative
- heterocyclic compound
- hypervalent S
- ketone
- ketone/aldehyde
- nitrile
- nitro compound
- nitrogen heterocyclic
- nitrohydrocarbon
- other
- phenol or hydroxyhetarene
- sulfide
- thiol
Email from Mike regarding opbendunit
Hi,
The MM2/MM3 force field parameter files in TINKER v. 5/6 use an opbendunit of 0.02191418 and so did Pengyu's early versions of the AMOEBA force field parameter files. On the other hand, current versions of the AMOEBA parameter files in TINKER5/6 do not use an opbendunit conversion. This will lead to problems if poltype output is appended to TINKER/FFX parameters.
What do you guys think? Does it seem easiest to standardize on the latest TINKER6 parameter files (ie. opbendunit = 1.0)? The poltype database of opbend parameters would need to be scaled by a factor of (1.0 / 0.02191418).
Thanks, Mike