Do you want to derive only the charges or all the parameters for that
modified residue? It all depends on how you want to derive them. If it is
the charges that you want to calculate, you can either create a model
where you only fit the modified region. Or you can follow the original
resp protocol describe in the following paper (check out page 20 for
parameterization of amino acids).
P. Cieplak, W.D. Cornell, C. Bayly & P.A. Kollman. Application of the
multimolecule and multiconformational RESP methodology to biopolymers:
Charge derivation for DNA, RNA and proteins. J. Comput. Chem. 1995, 16,
1357-1377.
http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/pdf
If you want to derive all the other force field parameters (such as bond,
angular, torsional terms as well as vdw) things will not be easy. I would
say the torsional parts would make sense to revise if it really is a
necessity.
Ilyas Yildirim, Ph.D.
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= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
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On Wed, 23 Apr 2014, Lara rajam wrote:
> Dear Amber Users !
>
> 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
>
> thank you
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>
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Received on Thu Apr 24 2014 - 06:30:02 PDT
