[AMBER-Developers] testing ff10

From: case <case.biomaps.rutgers.edu>
Date: Sun, 27 Mar 2011 22:00:51 -0400

On Sun, Mar 27, 2011, Jason Swails wrote:
> I decided to throw a little (not much) time at validating ff10 wrt what's
> written in the manual. I've written a little script to do this (attached
> here).


> As expected, the only ones that match (and match exactly through 100 steps)
> is the ff10/ff99SB for proteins (good news, no?).

Yes, confirming tests made here by InSuk Joung.

> For the other ones, I don't know what frcmods to load on top of ff99bsc0 in
> order to get what's "expected" for ff10.

According to the supplementary material from Banas10, you should do this:

 source $AMBERHOME/dat/leap/cmd/leaprc.ff99bsc0
 loadamberprep all_nuc94_ol_bsc0.in
 loadamberparams frcmod.ol.dat

The files for the last two lines are in amber11/dat/leap/ff99bsc0chiOL.
Setups created this way should then be tested against leaprc.ff10.

I'm really, really hoping that tec will chime in, since I think(?) he has
access to the "real" prmtops used for the tetraloop simulations reported
in the Banas10 paper. In addition, we want to be sure that we are really
doing the "right thing" with DNA as well. (A DNA setup with ff10 should be
identical to one from ff99bsc0.)


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Received on Sun Mar 27 2011 - 19:30:02 PDT
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