AMBER Archive (2008)

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

From: FyD (
Date: Wed Jan 02 2008 - 02:52:15 CST

Quoting John Chodera <>:

> 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.
> [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]

Well, you could apply what was done in the ref [1] and available in
[2] to recompute the charges using the parameters used by Duan et al.

For the procedure, see

In particular: For information about the Duan et al. FF see:

To compute charge values for central & terminal fragments see:

regards, Francois

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to