it's probably also worth looking at recent work from Piana and others
showing that the water models are also a major factor in modeling IDPs and
unfolded states. It probably isn't just the protein model.
On Wed, Jan 31, 2018 at 8:55 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> I believe Francesco Gervasio has developed at some point the files
> needed to use that force field in Amber. ... However, I recall from my
> initial attempts to use those files that they are incompatible with
> newer Amber versions because of atom type overlaps with newer Amber
> force fields .... So, even if you get the files from Francesco, I guess
> some work to adapt them to the newest Amber may be required .... Anyhow,
> in such cases please be very careful and make sure you will be using the
> correct parameters (e.g. by specific tests on your topology using parmed
> or other tools).
>
> I'd be curious to know why are you particularly interested in using that
> force filed for simulations of unstructured proteins ? ... I am not an
> expert in such simulations, but as far I recall from a review by Piana
> et al (Curr Opin Struct Biol 2014), the force field was not very good at
> describing the unfolded ensemble in protein folding simulations ....This
> may mean that its not that good with unstructured proteins either.
> Having said this, I believe some good agreement with NMR data was shown
> in a JACS paper 2012 by Lindorff-Larsen et al ... You may want to check
> more recent progress in the development of force fields for unstructured
> proteins ....
>
> But perhaps I am missing some details .... So, it would be nice to know
> the arguments for this force field ....
>
> Vlad
>
>
>
> On 01/31/2018 02:32 PM, David A Case wrote:
> > On Wed, Jan 31, 2018, Leena Aggarwal wrote:
> >> I am working with intrinsically disordered proteins and I want to use
> >> ff99SB*ildn force field. In Amber 12, I was able to use ff99SBildn force
> >> field but I was not able to use ff99SB*ildn force field.
> > It is still true that we don't distribute files for ff99SB*ildn.
> >
> > We do (as you have found) have files for ff99SBildn. If ff99SB*ildn is
> > a fairly small change, perhaps someone could make the required
> modifications.
> > Or maybe someone has already done that, and would be willing to share.
> >
> > ....dac
> >
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Vlad Cojocaru, PD (Habil.), Ph.D.
> -----------------------------------------------
> Project Group Leader
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> -----------------------------------------------
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
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Received on Wed Jan 31 2018 - 06:30:03 PST
