Thanks Lachele. No worries!
Emmanuel.
On Mon, Mar 15, 2010 at 9:39 AM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> 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
> >>>>>
> >>>>
> >>
> >>
> >>
> >>
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> >>
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> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Mon Mar 15 2010 - 09:00:05 PDT
