On Tue, 2014-09-16 at 18:34 +0200, Vlad Cojocaru wrote:
> 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?
I agree this could be useful if there was some type of coordinate
community effort amongst those that were interested in using these force
fields in Amber. I'll suggest Github as a helpful platform for anyone
that wants to take the "lead" on such an effort.
You can use the issue tracker for discussions and the Wiki and web site
for documentation. The files can be leaprc and frcmod files that users
can download separately from AmberTools that are still quite easy to
use.
Just a thought...
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 16 2014 - 10:30:02 PDT
