If it's really only or mostly us, then it's not that big a deal.
:-) Lachele
Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.ccrc.uga.edu
________________________________________
From: case [case.biomaps.rutgers.edu]
Sent: Tuesday, March 20, 2012 6:09 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] impose, ff12 and glycam tests
On Tue, Mar 20, 2012, B. Lachele Foley wrote:
>
> In any case, I don't really understand why that confuses leap, or why
> ROH confused leap. It seems that leap should be able to get that
> information from the context. Are there ever unit's in that location in
> that context? I suppose I could see what the code is doing. It seems
> like it should be fixable.
We could have LEaP force the arguments to impose to be strings. That is
inconsistent with the rest of LEaP, but maybe that's OK. But basically, the
manuals have always been wrong. You found that with the ROH vs OH stuff
(where an atom name and a residue name are the same), and it then popped
up with ff10, where "C" became the name of cytosine (as per PDB) as well
as the name for an atom. With OH and ROH, you had the option of changing
the residue's name, but we can't do that for "C", since both the residue and
the atom name are PDB standards.
I think this will have to be a patch for later. I also supsect that few
people outside glycam use impose (could be wrong, but leaprc.ff10 has been
available for over a year, and no one reported the problem you found.)
....dave
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Received on Tue Mar 20 2012 - 16:00:06 PDT
