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

From: Jason Swails <>
Date: Mon, 9 Mar 2015 15:01:34 -0400

On Mon, Mar 9, 2015 at 1:36 PM, David A Case <>

> 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).


> 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.


> 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 M. Swails
Rutgers University
Postdoctoral Researcher
AMBER-Developers mailing list
Received on Mon Mar 09 2015 - 12:30:02 PDT
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