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 Wed Apr 23 2014 - 23:00:02 PDT
