Phosphorylating a residue with Amber ff

From: Charles McAnany (
Date: Sat Nov 30 2013 - 12:24:19 CST


I'm in unfamiliar territory. I need to phosphorylate a few residues in a
short sequence I have (there's no structure for this peptide).
Looking at [1], it seems Amber force fields give the best results for
this sort of system, so I'd like to take my sequence, build it as a
straight chain (Molefacture), phosphorylate it (?), then simulate it
(namd). I have the straight-chain structure as a pdb, but I just don't
know how to start phosphorylating it. I see some patches in
toppar_all36_prot_na_combined.str, but these are CHARMM parameters, and
apparently AMBER is better for this run. (I also don't really understand
how PRES works.)

So, does anyone maybe have a reference that goes through how to do this?
If there's not a tutorial out there, I'd be happy to make one to add to
the tutorials section of the TCB site.

Charles McAnany.
Graduate student, Mura lab, University of Virginia.

[1] Cino, Elio A., Wing-Yiu Choy, and Mikko Karttunen. "Comparison of
secondary structure formation using 10 different force fields in
microsecond molecular dynamics simulations."/Journal of Chemical Theory
and Computation/8.8 (2012): 2725-2740.

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