AMBER Archive (2005)

Subject: Re: AMBER: Parameters for phosphorylated amino acids

From: Suxin Zheng (sxzheng_at_u.washington.edu)
Date: Thu Jun 23 2005 - 17:41:30 CDT

Any suggestion to find the parameters of dUMP(deoxyuridine-5'-
monophosphate)?

suxin

On Jun 23, 2005, at 7:24 AM, Nadine Homeyer wrote:

> Dear Amber users,
>
> we have calculated AMBER parameters for the most common phospho-
> amino acids in different protonation states and posted the
> parameter files to R. Bryce's AMBER parameter database (http://
> pharmacy.man.ac.uk/amber). The OFF and FRCMOD files, deposited in
> the database, can be used for the preparation of input files for
> phosphorylated peptides and proteins with the leap module of AMBER.
> A detailed description of the procedures used for the parameter
> calculation can be found in a paper that will be published in the
> Journal of Molecular Modeling soon.
>
> 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., 2005, in press.
>
> Regards,
>
> Nadine
>
> ___________________________________
>
> Abteilung f. Bioinformatik
> Institut f. Biochemie
> Emil-Fischer-Zentrum
> Friedrich-Alexander-Universitaet Erlangen-Nuernberg
> Fahrstr. 17
> 91054 Erlangen
> Germany
>
> Tel.: +49-9131-85-24675
>
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