Hi,
I have compared some short 500 step gas-phase simulations of the small
peptide systems DPDP and Ala10 using ff99bsc0 from AT1.4 and ff10 from
AT1.5 and can confirm that both the energies and the coordinates
match. The only differences in the parameter files are the number of
bond, angle, and atom types (I assume from additon of the 'CX' type).
I am testing larger systems now.
-Dan
On Sun, Mar 27, 2011 at 7:00 PM, case <case.biomaps.rutgers.edu> wrote:
> 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).
>>
>
> Thanks!!
>
>> 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.)
>
>
> ...thanks...dac
>
>
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Received on Wed Mar 30 2011 - 09:30:03 PDT
