Hi Chad,
You're in luck. Phosphorylated residues have been parameterized for the
AMBER force-fields (e.g. ff10, i.e. the protein force fields ff99/ff99sb):
N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht
J. Mol. Model. 2006, 12, 281-289.
AMBER force field parameters for phosphorylated amino acids in different
protonation states: phosphoserine, phosphothreonine, phosphotyrosine and
phosphohistidine
You can find the necessary library (.off) and frcmod files in the
collection maintained by the Bryce group in Manchester:
http://www.pharmacy.manchester.ac.uk/bryce/amber
So, you can simply:
- edit your pdb so that the TYR to be phosphorylated is renamed to Y1P or
Y2P (depending on the phosphate protonation state you want to model)
- download the .off and .frcmod files from the above website
- load these files and then your modified pdb in tleap/sleap/xleap and set
up your system as normal
Hope this helps,
Marc
On 28 November 2011 02:07, Petit, Chad <cpetit.email.unc.edu> wrote:
>
> Hi,
>
> I am new to Amber and was having trouble finding some information. I have
> searched the archive but have not seen a lot information from the
> beginner's perspective.
>
> Briefly, I would like to simulate the phosphorylated form of a protein for
> whom I only have a pdb of the non-phosphorylated form (tyrosine to
> phosphotyrosine).
>
> Is there any tutorials available that may shed some light on how to do
> this?
>
> Thanks
>
> Chad
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 28 2011 - 01:30:03 PST
