Lara,
I would use the same approach for generating a ff for "P-TYR" & "S-TYR"...
i. e.:
R-OH + Me-P/S -> R-O-"P/S"
(Tyr)
See
http://q4md-forcefieldtools.org/REDDB/projects/F-90/
You need to read
See the tutorials at
http://q4md-forcefieldtools.org/Tutorial
I can send you the web links of the last version of R.E.D. Server Dev.
and tutorial... Will be open soon.
regards, Francois
Quoting Lara rajam <lara.4884.gmail.com>:
> I checked P - TYR is in amber parameter data base .
>
> I am interested to know about the S - TYR ,
>
> how to proceed with this case ,
>
> since i got a note from earlier mail that i should not use the gaff for
> protein or DNA .
>
> so if one need to derive optimized geomentary QM is must or i can use the
> RESP server
>
> i am not clear . explain me more about building the library of these kind
> of amino acids
> On Thu, Apr 24, 2014 at 1:45 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Lara,
>>
>> > I would like to know if P-ser , S-Tyr , P-Tyr are already deposited in
>> the
>> > database
>>
>> phosphorylated amino acid residues are available in the amber force
>> field database. I wonder if they are not also in the amber
>> distribution as well; to be checked...
>> Sulfated-residues? I do not think so they are available.
>>
>> > or one have to do the partial charge derivation using QM to build the
>> amber
>> > force field parameters
>> > is general amber gaff is enough to do that .
>>
>> "gaff is enough to do that" : what does that mean?
>>
>> I would not use gaff for proteins and nucleic acids. A force field
>> designed for... proteins should be used instead; i.e. amber99SB or its
>> last adaptation available in the amber distribution.
>>
>> regards, Francois
>>
>>
>> > On Thu, Apr 24, 2014 at 12:38 AM, FyD <fyd.q4md-forcefieldtools.org>
>> wrote:
>> >
>> >> Dear Lara,
>> >>
>> >> Do you want to generate a force field (ff) for a whole molecule or for
>> >> a molecular fragment?
>> >> In general one wants to generate a ff for a molecular fragment...
>> >>
>> >> A fragment is empirical so it is designed from a whole molecule after
>> >> QM steps (geometry optimization and MEP computation) by applying
>> >> specific charge constraints on group(s) of atom(s) during the charge
>> >> fitting step (empirical step) and by removing the atoms involved in
>> >> these constraints...
>> >>
>> >> You can use R.E.D. Server Development at
>> >> http://q4md-forcefieldtools.org/REDServer-Development/ to generate ff
>> >> for whole molecules and/or molecular fragments.
>> >>
>> >> In this case you start by generating a PDB file for a dipeptide for
>> >> this modified amino acid (AA*); i.e. a residue with 2 peptide bonds
>> >> between this AA* and two capping groups (with well defined
>> >> conformation(s)): CH3CO-AA*-NHCH3 and you define charge constraints on
>> >> groups of atoms to generate the wanted fragments;
>> >> see http://q4md-forcefieldtools.org/Tutorial/images2/AA-residues.gif
>> >>
>> >> regards, Francois
>> >>
>> >> ps the P2N input file format is replaced by the PDB one in
>> >> REDServer-Development
>> >>
>> >>
>> >> > I have a doubt regarding force field generation for a modified amino
>> acid
>> >> >
>> >> > how one should take the atoms in the amino acid for running the QM .
>> >> >
>> >> > making this QM to build the amber force field ,
>> >> >
>> >> > so that the molecule is taken to the library and possibility to
>> generate
>> >> > the parameter for a PDB with these modified residues like it is done
>> for
>> >> > the default residues
>> >> >
>> >> > It will be helpful for me to understand if some one gives the detail
>> for
>> >> > the atom selections for the Qm run
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Received on Thu Apr 24 2014 - 00:00:02 PDT
