https://biomolmd.org/mw/index.php?action=history&feed=atom&title=Talk%3ALogs%3AparameterizationTalk:Logs:parameterization - Revision history2026-10-23T09:40:28ZRevision history for this page on the wikiMediaWiki 1.43.1https://biomolmd.org/mw/index.php?title=Talk:Logs:parameterization&diff=2102&oldid=prevEew947: Copied, haven't checked2025-04-21T23:15:10Z<p>Copied, haven't checked</p>
<p><b>New page</b></p><div>The list of Molecular Functional Groups used:<br />
#acid<br />
#alcohol<br />
#aldehyde<br />
#alkane<br />
#alkene<br />
#alkyl bromide (alkane w/ Br)<br />
#alkyl chloride (alkane w/ Cl)<br />
#alkyl iodide (alkane w/ I)<br />
#alkyne<br />
#amide (-NC=O)<br />
#amine （N w/ 1 lone pair)<br />
#arene<br />
#aromatic compound<br />
#aryl chloride<br />
#carbonitrile (-C#N)<br />
#carboxylic acid<br />
#cyclic hydrocarbon<br />
#ester (R -C(=O)O- R')<br />
#ether (R -O- R')<br />
#halogen derivative<br />
#heterocyclic compound<br />
#hypervalent S<br />
#ketone<br />
#ketone/aldehyde<br />
#nitrile<br />
#nitro compound<br />
#nitrogen heterocyclic<br />
#nitrohydrocarbon<br />
#other<br />
#phenol or hydroxyhetarene<br />
#sulfide<br />
#thiol<br />
<br />
==== Email from Mike regarding opbendunit ====<br />
<br />
Hi,<br />
<br />
The MM2/MM3 force field parameter files in TINKER v. 5/6 use an opbendunit<br />
of 0.02191418 and so did Pengyu's early versions of the AMOEBA force field<br />
parameter files. On the other hand, current versions of the AMOEBA<br />
parameter files in TINKER5/6 do not use an opbendunit conversion. This<br />
will lead to problems if poltype output is appended to TINKER/FFX<br />
parameters.<br />
<br />
What do you guys think? Does it seem easiest to standardize on the latest<br />
TINKER6 parameter files (ie. opbendunit = 1.0)? The poltype database of<br />
opbend parameters would need to be scaled by a factor of (1.0 /<br />
0.02191418).<br />
<br />
Thanks,<br />
Mike</div>Eew947