Dearest colleagues,
I would like to do classical MDS of a protein containing phosphorylated serines using GROMACS. Could someone point me in the direction of an accurate and modern force field supporting this?
Many thanks!
There are some pretty strong drawbacks to 53A6, most notably helix instability (fixed in 54A7, so it too can probably be extended). Modern AMBER and CHARMM force fields all support phosphorylated residues, as well. Our CHARMM36 port contains the -1 and -2 states for all phosphorylated amino acids.
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
For MDS of of a protein containing phosphorylated serines using GROMACS, you can employ an extended version of the GROMOS53a6 force field. Parameters for the phosphorylated serine can be taken from the GROMOS43a1 force field and implemented to the GROMOS53a6 force field. For further detail you can study this paper:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078472#s4
There are some pretty strong drawbacks to 53A6, most notably helix instability (fixed in 54A7, so it too can probably be extended). Modern AMBER and CHARMM force fields all support phosphorylated residues, as well. Our CHARMM36 port contains the -1 and -2 states for all phosphorylated amino acids.
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
If you plan on using the CHARMM force field, consider using the CHARMM-GUI input generator to facilitate the setup of your system.
http://www.charmm-gui.org/?doc=input/mdsetup
The Vienna-PTM webserver generates GROMOS 45A3 and 54A7 parameters for post-translational modifications, including phosphorylated serines. It also produces input files for GROMACS.
http://vienna-ptm.univie.ac.at/
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003154
Article Vienna-PTM web server: a toolkit for MD simulations of prote...
@Justin Lemkul Are the parameters for all phosphorylated residues available in the Feb 2016 release of the Additive force fields? I am planning on using them in NAMD and not Gromacs and unable to find the required parameters.
CHARMM-GUI has supported all forms of phosphorylated residues for years. They come from the CHARMM file toppar_all36_prot_na_combined.str (as patches).
@Justin Lemkul Thanks. Found them and they work properly. We have also parametrised a patch for N-terminal Acetyl Lysine. Where could we report it and/or send it to you for incorporation in the CHARMM force field?
The phosphorylated residues need to be added to residuetypes.dat as Protein types, otherwise pdb2gmx will incorrectly start new chains when it runs into them and you get problems like this related to terminus construction.
Also you can simply place the modified residuetypes.dat into the working directory.
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