Hi,
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?
Thanks a lot,
Krisztina
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Received on Thu Sep 20 2012 - 04:30:02 PDT
