Re: [AMBER-Developers] force-field naming (redux)

From: Christina Bergonzo <cbergonzo.gmail.com>
Date: Mon, 9 Mar 2015 08:09:47 -0600

Hi,

To address Dave's 2nd point, I had added Table 3.2, How to specify
available Nucleic Acid force fields in LeAP. A PDF is attached. Here I
assumed loading leaprc.ff14SB was Amber's "default" behavior. I like that
the references are matched up with the leaprc files, so it should be
crystal clear what parameters are being used for the leaprc loaded, making
it easier to cite in manuscripts as well.

Maybe something like this could be expanded to include all biomolecules
Amber provides force fields for, as well as a section which includes what
we recommend for combinations like protein+DNA/RNA. If the naming
conventions are changed before the release, the table should of course be
updated.

-Christina

On Sun, Mar 8, 2015 at 7:31 AM, David A Case <case.biomaps.rutgers.edu>
wrote:

> We have not yet addressed the problem of force field naming that was
> brought
> up at the Amber developers' meeting in February. Some notes:
>
> 1. Section 3.2.1 of the manual still reads as though ff14SB is only for
> proteins. There is one tiny sentence, many paragraphs later, that
> indicates
> it could also be used for RNA; nothing about whether it might be good for a
> combination of proteins and nucleic acids.
>
> 2. Table 3.1 is not as helpful to users as it should be. It lists of
> bunch
> of modifications, but gives no indication of *how* to load any of the force
> fields that are listed there.
>
> 3. We talked about having separate leaprc files for proteins, DNA and RNA,
> but Jason has noted potential problems with this. I don't have a suggested
> solution (and I've not really heard one): but we need very soon to come to
> some agreement, and to have appropriate leaprc files for various
> recommended
> combintations of parameters.
>
> 4. On a related topic: we need a better way for a user to specify water
> and
> ion parameters. Specifying TIP3P water should automatically load the
> associated ion paramters; same for other supported water models. This
> should
> probably be implemented by having a leaprc.tip3p that performs these
> actions.
>
> 5. (I can do this one): the beginning of section 3.1 should probably
> suggest
> to people that they load a "leap.in" file, which in turn would load
> *several*
> leaprc files for the components they need. That is, the "standard" would
> be
> to expect to load at least a protein and a water/ion file; if there are
> ligands, one would usually load leaprc.gaff; if one has lipids
> or nucleic acids or carbohydrates, one would load additional files.
>
> Suggestions are both welcome and needed....thx...dac
>
>
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>



-- 
---------------------------------------------------------------------------------------
Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652 / Fax: (801) 585-6208
---------------------------------------------------------------------------------------



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Received on Mon Mar 09 2015 - 07:30:08 PDT
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