yes that is correct. the bsc0 and 99SB corrections are independent, so
neither paper mentions the other. we just apply both.
On Mon, Mar 22, 2010 at 11:20 AM, Alan <alanwilter.gmail.com> wrote:
> So I read parmbsc0 paper and has no mention at all to ff99SB.
>
> >From what Case said:
>
> "Just a note: this combination is what you get if you use the
> (poorly-named?)
> leaprc.ff99bsc0."
>
> So I am assuming that leaprc.ff99bsc0 contains the fixes done in ff99SB
> over
> ff99.
>
> Is it correct?
>
> Thanks,
>
> Alan
>
>
>
> On Mon, Mar 22, 2010 at 15:04, mattia <mori.dott.gmail.com> wrote:
>
> > Hi,
> > I think this is really true for a general system.
> > In my case I introduced custom zinc binding residues, whose atom point
> > charges were calculated with a DFT approach. This is the reason for the
> > usage of ff03 instead of ff99SB for the protein side. However the system
> was
> > working finely.
> >
> > cheers
> >
> > Mattia
> >
> >
> >
> >
> > Carlos Simmerling ha scritto:
> >
> > 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
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >
> > _______________________________________________
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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 - 09:00:03 PDT
