Emmanuel,
Sorry so long getting back to you... Being amino acids, they were
developed for the default Amber values (1.2 and 2.0).
:-) L
On Sat, Feb 27, 2010 at 8:29 PM, Emmanuel Baribefe Naziga
<baribefe.gmail.com> wrote:
> 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
>>>>>
>>>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 15 2010 - 09:00:04 PDT
