The ff99sb*-ildn appeared in the tests by D.E. Show and coworkers to perform the best in their folding simulations. That's where the desire of using this force field comes from (including mine). Unfortunately , this variant was never available in Amber (only in Gromacs). In my lab we went for the Buschweiler modifications instead of Best and Hummer thinking that they have the same phylosophy but serious tests are still missing and we dont know if they behave the same. The new ff12sb and ff14sb are still under scrutiny.
It is unfortunately not possible for each of us to test the different versions and if we want to use a force field that does best in reproducing secondary structure stability.
I think it would be very useful a blogging platform where new tests with new force fields can be placed, esspecialy if these force fields are distributed ... Without such a platform, we'd have to rely only on published data and we all know how slow publications are ... Of course, the dilema would be how to publish on such a blogging platform without jepartising publication of the new ff versions ... Maybe a closed platform which people can access only with a userid and password?
Best
Vlad
On September 16, 2014 6:06:44 PM CEST, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>I agree with Dave, these can be tricky. For example, an article by Best
>et
>al. in 2008 (DOI: 10.1529/biophysj.108.132696) concluded that ff99SB
>performed poorly among the force fields they had tested, but this was
>due
>to incorrect implementation and the conclusion was subsequently
>reversed
>(see DOI: 10.1016/j.bpj.2009.04.063
><http://dx.doi.org/10.1016%2Fj.bpj.2009.04.063> for additional
>details).
>carlos
>
>On Sun, Sep 14, 2014 at 7:46 PM, David A Case
><case.biomaps.rutgers.edu>
>wrote:
>
>> On Sat, Sep 13, 2014, Thomas Evangelidis wrote:
>>
>> [Mentions force fields he would like to try, including
>> ff99sb*, ff03*, ff99sb*-ILDN, charmm22*, ff03w+TIP4P/2005]
>>
>> > Unfortunately, I do not have the time, neither
>> > the technical support to port myself these force fields into AMBER.
>>
>> It can be tricky to get everything correct. The 2009 Best/Hummer
>> modifications involve only corrections to the psi angle, but you have
>to
>> make sure that they are not applied to glycine or proline. I'm not
>sure
>> that this can be done inside tleap without making some new atom types
>that
>> are specific to GLY and PRO. This might be a place where a ParmEd
>script
>> could be of real use.
>>
>> If users have files that enable these force field modifications, we
>can
>> certainly add them to the distribution, or post them on the web site.
> But
>> I
>> also second Carlos' comments about ff14SB, and that there is no
>single
>> "best"
>> force fields.
>>
>> ...dac
>>
>>
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>>
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Received on Tue Sep 16 2014 - 10:00:02 PDT
