Thanks Francios, Lachele
Another question please. My goal is to simulate a glycosilated proline like
peptide using GLYCAM parameters for the sugar hence the questions about the
charge derivation methodology of OLP etc. I would like to ask to confirm
that using a vdW and NB scaling of 1.0 as is recommended for use with GLYCAM
is the ideal thing to in this case since the charge derivation is somewhat
more GLYCAM oriented.
Many thanks.
Emmanuel.
On Sat, Feb 27, 2010 at 10:10 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 - 17:00:02 PST
