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 - 09:30:03 PST
