Hi Lachele
Thanks very much for this information. I suppose the CHelpG algorithm was
used for the MEP calculation.
Emmanuel.
On Fri, Feb 26, 2010 at 8:56 AM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> Emmanuel,
>
> The person who did the work reports the following. He also says that,
> yes, it is a one-stage resp fitting.
>
> ==================================
> Charges were developed for three hydroxyproline structures:
> N-terminal, internal and C-terminal.
> - The N-terminal residue was capped with N-methyl (CH3-NH-) at the
> C-alpha atom, while the pyrolidine ring nitrogen atom was protonated.
> - The internal residue was capped with CH3-NH- and an acyl group
> (CH3-CO) at the C-alpha atom and pyrolidine ring nitrogen atom,
> respectively.
> - The C-terminal residue was capped with CH3-CO at the ring nitrogen
> atom, and a carboxylate at the C-alpha atom.
>
> 1). Charges were computed at the HF/6-31G*//HF/6-31G* level with a
> RESP charge restraint weight of 0.001
> 2). During the RESP charge fitting, the charges of the backbone atoms
> (N, CA, C, and O), were restrained to those of proline found in the
> all_amino94.in file. Also, the charges of the CH3-CO and CH3-NH groups
> were restrained to the values in the all_amino94.in file.
>
> Hope that helps ...
> ==================================
>
> Please let us know if you need further information.
>
> :-) Lachele
>
> On Thu, Feb 25, 2010 at 12:33 PM, Emmanuel Baribefe Naziga
> <baribefe.gmail.com> wrote:
> > 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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>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Fri Feb 26 2010 - 08:30:04 PST
