Why a canonical AMBER simulation of DNA doesn't include dangling 5' phosphate? So, if I want to simulate an oligomer of length N bp, then it will have 2N bases but 2(N-1) phosphate when standard AMBER protocol is applied.
However, after some googling, I found GROMACS does consider these dangling phosphates. I could not find a proper explanation for this.
Unless the 5'-terminal phosphate group is the object of interest, 5'-OH group is better because, compared to the phosphate group, the hydroxyl group contains atoms with smaller partial atomic charges.
i have AMBER 94 force field parameters (in a format for the Q molecular dynamics simulation package) for standard 5'-terminal dexoyribonucleotide-5'-phosphates . . .
in amber , charm, and namd packages, you can add patch to phosphate group, you can review manul of this programs.
Ropón-Palacios G. Hi Ropen, could you please suggest a tutorial to do that?
Thank you
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