On Fri, 2013-11-01 at 11:22 -0600, Daniel Roe wrote:
> Hi,
>
> I think there are really two issues here. One is the somewhat
> arbitrary way that LEaP assigns GB radii, the other is that there is
> (at least I think) no definitive database for all Amber atom types.
>
> A google search for "amber atom type" brings up several results, but
> other than the GAFF page there are no results from ambermd.org (at
> least on the first page). I think there needs to be a central data
> base of Amber atom types (including GAFF, GLYCAM, etc). This way
> anyone developing new parameters has one place to check for existing
> atom type names (as well as guidelines on how to create type names). I
> know there has been talk of doing this in the past, but I'm not sure
> if any progress has been made.
Lachele put together a nice table that's in the
doc/AtomTypesTableWorkspace.lyx file. It is a long list that appears to
have taken a long time to put together. It includes most of the force
fields (except ff13, it appears). It was added to the repo Feb. 2, 2012
and last updated (by Lachele) Feb. 23, 2012. Those were 2 of the only 3
commits (together with James' addition of ff12SB atom types).
This was an excellent start, but unfortunately probably suggests to me
that either the central database will not work, or the lyx table is the
wrong medium to be using given its lack of attention and notoriety. I'd
love to see it on the Wiki, but Amber's wiki seems to me to be (sadly)
underutilized and there is no user-space Wiki to make it more widely
available.
> As far as assigning GB radii, I agree with Jason that the long term
> solution is to assign parameters like these based on chemical
> knowledge. I think the easiest way to do this going forward may be to
> have an additional atom type parameter that is the unambiguous atom
> type based solely on chemical environment; i.e. something like 'sp3
> carbon' == 'Amber type CT' == 'GAFF c3' == unambiguous type 0, 'amide
> H' == 'Amber type H' == 'GAFF hn' == unambiguous type 1, etc.
This already exists to some extent in LEaP. Each atom knows about its
hybridization, number of bonded partners, and atomic number. Hopefully
this is enough to unambiguously assign GB parameters?
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 01 2013 - 11:00:02 PDT
