Hi Mark,
On Dec 3, 2006, at 7:20 AM, Mark Abraham wrote:
So evidently opls_005 is a nitrogen atom... so what's with the "C2
6"?
Further, there is no bonded interaction in ffoplsaa.rtp for "C2", but
there is C_2... So I really don't understand what is going on.
The "6" doesn't belong to the bonded_type; it's the atomic number of
the atom type (or heavy atom, in the case of united atoms) and used
for QM/MM stuff. We added it to most force fields with a script, but
apparently forgot to update the comment.
The other problem is that this data originally comes from Bill
Jorgensen's distribution, and it's not entirely complete. For a
start, the first 65 atoms are for the united atom force field, and
most of these do not have complete bond information (since the
original parameter files were the all-atom opls version).
I still decided to keep atoms 1-65 for two reasons: First, I couldn't
see any good reason to remove them when they only used 65 lines, and
second there are a couple of useful ones without bonds (united-atom
CH4, ions, etc.).
However, and this is the good news, OPLS bonds and angles are
essentially amber, and the united-atom ones likely correspond to
amber. The only exception here is for the newer torsions, where we
have also had to introduce some extended types (anything X_2 is
derived from X) where Bill introduced "exceptions" for particular
residues or atoms.
If you need to automate conversion, my first recommendation would be
to cut atoms 1-65 and try again!
Cheers,
Erik
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
