Thank you very much dear Carlos.
Indeed, I was waiting you to stand up and enlighten this discussion.
Just one thing more, would you have recent references on MD with bsc0 and
ff99SB?
It's my fault as well that I haven't read the bsc0 paper yet. Rectifying it
now..
Cheers,
Alan
On Mon, Mar 22, 2010 at 14:24, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I think this is not a good idea. ff99SB for nucleic acids is the same as
> ff99 (SB only changed proteins), and ff99 had problems that are well
> documented in the literature. the force field to use for nucleic acids (in
> my opinion) is the bsc0 modification to ff99SB. In my protein-DNA work I
> use
> ff99SB for proteins and bsc0 for nucleic acids.
>
> I would NOT mix ff03 and ff99SB, they are different charge models and
> nobody
> has validated the combination. besides, since ff99SB performs better for
> proteins in most comparisons, there is no need to mix ff03 charges with
> those in ff94/99/99SB, which are all the same for charges.
>
> On Mon, Mar 22, 2010 at 9:08 AM, mattia <mori.dott.gmail.com> wrote:
>
> > Hi,
> > For sure you have to minimize the protein structure (and the solvent, if
> > present), before to attempt MD simulations.
> > For a similar system (protein-DNA) I've succesfully used ff99SB for
> nucleic
> > acids and ff03 for the protein, modified with Zn-binding parameters
> [Mori M
> > et al., J Chem Inf Model. 2010 Mar 4. (Epub ahead of print)]. Just load
> both
> > of them in leap module.
> > About the version of Amber, I've used without problems AMBER10. I think
> > the MMPBSA test problem has been already fixed, check the archive.
> > However Amber9 should also works fine.
> > Regards
> >
> > Mattia
> >
> >
> >
> >
> >
> > geyan ha scritto:
> >
> > Hi all amber users,
> >> I want to do MD about a system of proteins and DNA complex. Before
> the
> >> MD,I think the first step is to minimize the protein 3D structure which
> is
> >> produced by homology modelling.
> >> My question is choosing which force field for protein,which one for
> >> DNA, and which one for the complex?all using ff99SB?
> >> By the way,amber9 and amber10,which one is better?I have heard of
> many
> >> unexpected problems for amber10 and I met one in MM_PBSA test
> >>
> >> --------------
> >> geyan
> >> 2010-03-22
> >>
> >>
> >>
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> >>
> >>
> >>
> >
> >
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--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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Received on Mon Mar 22 2010 - 08:00:03 PDT
