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 - 22:00:02 PDT
