Dear Krisztina,
> I would like to run MD on a DNA 14mer containing a modification on a
> base: a covalently attached amino acid. My question is: can I use
> GAFF atom types and parameters derived with antechamber and add to
> the AMBER ff? The critical part is probably the linker connecting
> the nucleotide to the amino acid. Can the AMBER ff and small organic
> GAFF types be used together or I need parameter optimisation?
You will have to generate a molecular fragment starting from a whole molecule.
Thus, you might be interested in using R.E.D. at q4md-forcefieldtools.org.
You will find tutorials there as well.
As you will use the last version of the Amber FF for nucleic
acids/proteins my feeling is that you should keep using this FF for
your modified nucleoside/tide as well; i.e. I would not use GAFF.
regards, Francois
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Received on Thu Sep 20 2012 - 09:00:03 PDT
