Dear Lachele & Emmanuel,
You will find many examples (submitted end of 2005) of such charge
derivation approaches in R.E.DD.B. (using different algorithms in MEP
computation & various fitting procedures).
See for instance: http://q4md-forcefieldtools.org/REDDB/projects/F-1/ &
F-2, F-3, F-4, F-5, F-6 etc...
scf=tight is not required: This can save substantial cpu time when
building a force field topology database.
regards, Francois
Quoting "Lachele Foley (Lists)" <lf.list.gmail.com>:
> #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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Received on Sat Feb 27 2010 - 09:30:02 PST
