Here is Jason's reply to the question about the OPLSAA atom numbers.
He can be reached at [email protected]
If there is a particular convention we should be following with
respect to the OPLSAA atom type numbers, or website we should link to
for the original oplsaa.prm parameters, please post a reply.
Just a follow-up note on this issue:
It does look like the atom-numbers and force-field parameters do
indeed come from an earlier version of the "oplsaa.prm" file that
comes with TINKER:
So I deleted the "oplsaa.txt" file from the moltemplate distribution
and replaced it to a link to those files (and I made some
modifications to the "oplsaa_moltemplate.py" script so that it can
handle those files too).
Anyway, the file links above presumably have more up-to-date versions
of these parameters. So if you use OPLSAA, you should use them
instead of the original "oplsaa.txt" file which came with moltemplate
This will change all the atom-numbers as well.
All of these changes have been made to the code and the examples which
come with moltemplate v1.21 (released today).