Re: [AMBER] Charge protocol for OLP, HYP

From: Lachele Foley (Lists) <"Lachele>
Date: Mon, 15 Mar 2010 11:39:31 -0400

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_amino9