amber-developers: Re: Ff02 pol

From: David A. Case <>
Date: Mon, 10 Nov 2003 17:21:18 -0700

On Mon, Nov 10, 2003, Yong Duan wrote:
> Just to let both of you know that I, after series of delays, finally
> resumed my tests on ff02/pol. I think the preliminary data appears to
> suggest a bias toward beta-extended regions (including PPII region).
> Again, it is Ace-Ala4-Nme in water. This sparse data set was collected
> over about 3.5 ns after 2ns equilibration. I will try to accumulate more
> data. I used Junmei's latest parm99mod2 without EP. Let me know if you
> have any suggestions.

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
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,
am not sure, that it doesn't really matter in this case whether one
parm94 or parm99, but that needs to be checked.]

I think it is better to use parm94.dat/parm99.dat + frcmod.ala3_refit.
whole idea is to have "standard" parm files (which change only
plus frcmod files for testing changes. (This is a moot point here; more
a suggestion for the future.)

3. It's not clear to me that anyone would think that these parameters
    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
    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
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
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
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Received on Wed Apr 05 2006 - 23:50:08 PDT
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