AMBER Archive (2008)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Jan 02 2008 - 02:52:15 CST

Quoting John Chodera <jchodera_at_gmail.com>:

> 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] http://pharmacy.man.ac.uk/amber/

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
http://structbio.vanderbilt.edu/archives/amber-archive/2007/4747.php

In particular: For information about the Duan et al. FF see:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#7

To compute charge values for central & terminal fragments see:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#11

regards, Francois

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