#hf/6-31g* pop=chelpg iop(6/33=2) scf=tight
(Gaussian)
On Fri, Feb 26, 2010 at 11:28 AM, Emmanuel Baribefe Naziga
<baribefe.gmail.com> wrote:
> 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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Feb 26 2010 - 10:30:02 PST
