AMBER Archive (2008)

Subject: AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine

From: John Chodera (jchodera_at_gmail.com)
Date: Tue Jan 01 2008 - 19:44:34 CST

Happy New Year, all!

Has anyone developed ff03-consistent parameters/charges for
phosphorylated amino acids? I've noted at least one published set for
ff94/ff96/ff99/ff99sb-compatible parameters [1] (conveniently
collected in the contributed parameters database [2]) but haven't come
across a ff03-consistent set.

For the curious, we're interested in fiddling with free energy
calculations to phosphorylated and unphosphorylated forms of MAP
kinases.

Cheers,

John

[1] N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht. AMBER force field
parameters for phosphorylated amino acids in different protonation
states: phosphoserine, phosphothreonine, phosphotyrosine and
phosphohistidine. J. Mol. Model. 2006, 12, 281-289.

[2] http://pharmacy.man.ac.uk/amber/ 

--
Dr. John D. Chodera <jchodera_at_gmail.com>      | Mobile    : 415.867.7384
Postdoctoral researcher, Pande lab            | Lab phone : 650.723.1097
Department of Chemistry, Stanford University  | Lab fax   : 650.724.4021
http://www.dillgroup.ucsf.edu/~jchodera
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