RE: amber-developers: Re: Ff02 pol

From: Yong Duan <>
Date: Mon, 10 Nov 2003 19:05:19 -0700

Thanks for the comments.

Will stop parm99MOD2 test (which is clearly not intended for ff02pol).
Will test on parm99/ff02pol parm99/ff02ep_pol combinations. Both
probably should be tested, if we include them in the distribution,
although the argument for ff02ep_pol is indeed strong. The users (and
ourselves) should know what to expect.

Frcmod.ala3_refit is Carlos' mainchain torsion (same as parm99MOD2.dat).

I used POL3BOX.

> Several comments from my side:
> 1. This discussion should take place on,
> since it is relevant to everybody. I'm sending this
> message there.
> 2. The "parm99MOD2.dat" file in the amber8 tree (I assume
> this is what you
> meant) is not from Junmei, but rather was created by Alexey
> Onufriev, based on
> the parameters from Simmerling, Strockbine, Roitberg, JACS
> 124:11258, 2002, at
> least as far as I can tell. It actually takes the mods that
> Carlos/Adrian
> applied to parm94.dat, and applies them to parm99.dat
> instead. [I think, but
> am not sure, that it doesn't really matter in this case
> whether one patches
> parm94 or parm99, but that needs to be checked.]
> I think it is better to use parm94.dat/parm99.dat +
> frcmod.ala3_refit. The
> whole idea is to have "standard" parm files (which change
> only occassionally)
> plus frcmod files for testing changes. (This is a moot point
> here; more of
> a suggestion for the future.)
> 3. It's not clear to me that anyone would think that these
> parameters should
> be good for polarizable calculations(?). I don't know
> that they have
> ever been tested that way.
> 4. If we are going to test polarizable ff's, in my opinion
> it should really
> be done with EP's. I suppose we could do both with and
> without EP's,
> but then we lose the H-bond directionality advantages of
> the EP stuff.
> 5. What water model are you using?
> Comments from other force-field knowledgeable people are solicited!
> [Aside: I've been looking at the notes we made in July for
> renaming the force
> field files to a more systematic notation. I am kind of
> waiting for Tom
> Cheatham to split apart the protein and nucleic acid files,
> so that we can "mix
> and match" these as we discussed at the meeting.]
> ..thanks for the update!.....dac
> --
> ==================================================================
> David A. Case | e-mail:
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA |
> ==================================================================
Received on Wed Apr 05 2006 - 23:50:07 PDT
Custom Search