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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Received on Tue Sep 16 2014 - 09:30:02 PDT
