AMBER Archive (2006)

Subject: RE: AMBER: ff03 and ff99SB force fields

From: Yong Duan (duan_at_ucdavis.edu)
Date: Thu Aug 03 2006 - 14:29:51 CDT

To follow up on this thread, Carlos is absolutely right that one should not
simply mix two charge models.

However, if the concern is only limited to the terminal residues, the answer
is much less a clear cut. Although ff03 charges were based on a different
model, they are reasonably compatible with the Cornell charges, as far as
the dipole moments and other simple measures are concerned. In our lab, we
simply use the ff94 charges for the terminal groups for most of the
simulations. However, in the cases where the terminal charges are
anticipated to play crucial roles, we try to refit the charges. For example,
when we try to compare the energies of di-peptides against QM energies, we
use the ff03 charges for the amino acids and fit the charges for the
terminal groups. In this case, the terminal groups do have different charges
according to the amino acid they are attached to. But such an approach is
considered unecessary for larger peptides. If the application is to
proteins, I'd be less concerned.

Please also keep in mind that the charges of the terminal groups in the
Cornell charge set were obtained by a retro-fitting using a combined-fit
scheme (with NMA?), rather than from the fitting of the individual terminal
amino acids.

Hope this helps. Please do let us know if you have any further questions.

yong

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Carlos Simmerling
> Sent: Thursday, August 03, 2006 3:59 AM
> To: amber_at_scripps.edu
> Subject: AMBER: ff03 and ff99SB force fields
>
>
> Vlad,
> I'm replying off the list to send you the manuscript
> for the ff99SB article that is in press at Proteins.
> For the purposes of the archive, I'll clarify my comments on
> compatibility and invite Yong Duan to join in and give us the
> benefit of his much more extensive experience with ff03.
>
> I think that one has to be extremely careful mixing force fields.
> To my knowledge it has not been demonstrated that hydrogen
> bonds (for example) between ff94 and ff03 backbone charges
> are the same as ones between pairs of ff03 groups. Since the charge
> model fundamentally differs (or else why is there a need for
> ff03?) one
> should probably not mix them in a single simulation. It would be like
> taking
> charmm parameters and using with ff94- both are internally
> consistent but
> you need to carefully test whether they have the same intra-
> and inter-
> force field interactions.This is important to me since one of
> my projects
> involves protein/DNA complexes and I don't want to do all of the
> extensive testing needed to make sure that the DNA parameters will
> work well with ff03 proteins when I know that ff99SB doesn't have
> that concern.Another concern about ff03 is that not all of the
> torsions were refit. I don't mean to criticize Duan's effort at all,
> just to
> point out that I think ff03 is still a work in progress (and
> a good one).
>
> Our ff99SB paper is in press at Proteins. I believe that we
> do as well
> or even
> slightly better than ff03 for the things you ask about. Both
> ff99SB and
> ff03 are
> much better than any of the other Amber variants that we
> tested. In addition
> to secondary structure bias, almost all of the other have very serious
> problems with their glycine parameters.
> Carlos
>
> Vlad Cojocaru wrote:
>
> >Dear Carlos,
> >
> >I am following closely this discussion about the incompatibilities
> >between ff03 and the other amber force field versions. So,
> first I would
> >like to ask you, what do you actually mean by "imbalance in
> elecrostatics".
> >
> >Furthermore, the paper describing the ff03 speaks of
> correlation between
> >the "new" charges and the old charges and claims that at
> least in cases
> >of ligand-protein interactions, there should be no reason not to use
> >"old" ligand charges with "new" charges for protein residues.
> >
> >Moreover, when ff03 is loaded into Leap, only non-terminal
> amino acids
> >are loaded from the new library, while N-terminal and
> C-terminal AA are
> >loaded from the old 94 libraries. So, isnt that
> inconssistent? Or is it
> >believed that non-terminal residues are not that important?...
> >
> >The reason for asking these questions, is because according
> to studies
> >that have been done in our group (not by me), ff03 seems to be by far
> >the best version if one is interested in lifetimes and stabilities of
> >secondary structural elements (ff99SB was not tested). Is there any
> >reference which compares ff99SB with ff03 in that respect?
> >
> >Best wishes
> >vlad
> >
> >Carlos Simmerling wrote:
> >
> >
> >
> >>due to the different charge model, you will need to find parameters
> >>developed specifically for ff03. using other sets would result in
> >>imbalance in electrostatics between different groups and is not
> >>a good idea. On the other hand, ff94, ff96, ff99 and several other
> >>variants such as our lab's ff99SB and parameters from Garcia and
> >>Pande all use the same charge model and will work with any
> parameters
> >>developed for ff94.
> >>
> >>Zu Thur Yew wrote:
> >>
> >>
> >>
> >>>Hi,
> >>>
> >>>I would like ask if there are any pTHR parameters suitable for use
> >>>with ff03?
> >>>
> >>>I know there are parms developed in the same way as ff94/ff99...the
> >>>charges for normal THR in ff99 & ff03 seems quite different...
> >>>
> >>>has anyone any experience using these parms with ff03?
> Would problems
> >>>be expected if these parameters are used with ff03?
> >>>
> >>>Any advice would be most appreciated!
> >>>
> >>>Many Thanks,
> >>>
> >>>ZT
> >>>
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> >>
> >
> >
> >
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