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 - 08:00:04 PST
