Thanks. Does this mean that it a one stage RESP fit with the 0.001 weight
not the usual 2 stage?
Emmanuel.
On Thu, Feb 25, 2010 at 10:27 AM, Lachele Foley (Lists)
<lf.list.gmail.com>wrote:
> Ok. Got more info.
>
> The charges were generated using hf/6-31g* (resp weight of 0.001)
> from a single, optimized structure (standard FF99 method in paper
> below). Charges are on all atoms. You might gain additional insight
> from the Pande paper Carlos mentioned.
>
> "Standard FF99": Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C,
> Alagona G, Profeta S, Jr., & Weiner P (1984) Journal of American
> Chemical Society 106, 765-784.
>
> Let me know if you have other questions.
>
> :-) Lachele
>
>
> On Wed, Feb 24, 2010 at 10:36 AM, Emmanuel Baribefe Naziga
> <baribefe.gmail.com> wrote:
> > Thanks everyone
> >
> > As Carlos mentioned I am looking for information specific to OLP/HYP
> > derivation such as what Lachele provided although I have also considered
> the
> > RED methodology. I have read the 2008 JCC paper but have not find
> specific
> > information about charge derivation for the non carbohydrate residues in
> > GLYCAM06. Its a huge paper maybe I am missing something!
> >
> > Lachele please let me know if you get information that throws more light
> on
> > this.
> >
> > Thanks again.
> >
> > Emmanuel.
> >
> > On Wed, Feb 24, 2010 at 7:59 AM, Lachele Foley (Lists) <
> lf.list.gmail.com>wrote:
> >
> >> Lachele> maybe a glycam person can add info here...
> >>
> >> Sorry... was checking stuff. I'm pretty sure that the backbone
> >> charges were based on ff94 and the rest of the charges were determined
> >> using the ensemble averaging procedure outlined in the paper below.
> >> But, I'm checking with the relevant folks now to make sure that's what
> >> actually happened.
> >>
> >> General charge method is in here: JOURNAL OF COMPUTATIONAL CHEMISTRY
> >> Volume: 29 Issue: 4 Pages: 622-655. 2008
> >>
> >>
> >>
> >> On Wed, Feb 24, 2010 at 9:28 AM, Carlos Simmerling
> >> <carlos.simmerling.gmail.com> wrote:
> >> > i think the question was about how the glycam OLP/HYP charges were
> >> derived.
> >> > did they use REDDB?
> >> > maybe a glycam person can add info here...
> >> >
> >> > if it was just about how it has been done in general, the work by
> Pande
> >> and
> >> > others on HYP could be a good place to start, it's been published
> >> >
> >> > On Wed, Feb 24, 2010 at 9:20 AM, FyD <fyd.q4md-forcefieldtools.org>
> >> wrote:
> >> >
> >> >> Dear Emmanuel,
> >> >>
> >> >> Can someone please point me in the direction if a reference for the
> >> charge
> >> >>> derivation protocol employed in getting charges for OLP, HYP in the
> >> >>> GLYCAM
> >> >>> forcefield?
> >> >>>
> >> >>
> >> >> You might look at the "F-85" R.E.DD.B. project (among many others)
> where
> >> >> you will find references & examples/discussions about charge
> derivation.
> >> >>
> >> >> regards, Francois
> >> >>
> >> >>
> >> >>
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> >>
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >>
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>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Thu Feb 25 2010 - 10:00:03 PST
