On Mon, Mar 9, 2015 at 1:36 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Mon, Mar 09, 2015, Christina Bergonzo wrote:
> >
> > 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.
>
> Kudos to Christina for actually proposing something concrete.
!!
> Since there is
> only one entry in the "load this frcmod" column, may that could be put the
> the
> Notes column, and third column eliminated, to make things easier to read.
>
> Here's one idea I have:
>
> 1. Remove the following lines from leaprc.ff14SB (and similar files):
> #
> # Load water and ions
> #
> loadOff atomic_ions.lib
> loadOff solvents.lib
> HOH = TP3
> WAT = TP3
>
+0.5 -- I would also support a "default" choice of water, if any consensus
can be made, along with the corresponding default choice of water model.
> 2. Create instead leaprc.{tip3p,spce,tip4pew} files that include the
> appropriate lines and the appropriate ion frcmod files. (Someone has to
> decide what the most "appopriate" ions are here).
>
+2
> 3. Also create leaprc.1264.{tip3p,spce,tip4pew} for the 12-6-4 variants of
> the ion parameters. Figure out what is mostly likely to helpful for users,
> and relegate the "hfe"/"iod" distinctions to expert use.
>
+1
> With this idea, someone running a GB simulation would just load
> leaprc.ff14SB;
> someone wanting to run an explicitly solvated simulation would add load one
> of the water/ion leaprc files. We would no longer have a default water
> model.
>
> This proposal would indeed break existing workflows; comments about how
> big a
> deal this might be are welcome.
>
I think this deserves a new leaprc file, personally.
People that still use "leaprc.ff14SB" will still get their "old" behavior
that won't break workflows. People that use the new, recommended force
field leaprc will get the 'newer' behavior.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 09 2015 - 12:30:02 PDT
