AMBER Archive (2006)

Subject: Re: AMBER: LEaP not recognising Phosphate group in TYR

From: David A. Case (case_at_scripps.edu)
Date: Sat Dec 02 2006 - 11:52:44 CST

On Sat, Dec 02, 2006, bertrand russell wrote:

> FATAL: Atom .R<NMET 1>.A<H 20> does not have a type.
> FATAL: Atom .R<TYR 189>.A<HB1 22> does not have a type.
> FATAL: Atom .R<TYR 189>.A<HZ 23> does not have a type.
> FATAL: Atom .R<TYR 189>.A<P 24> does not have a type.
> FATAL: Atom .R<TYR 189>.A<OP1 25> does not have a type.

The names in your db file, have to match those in the Amber libraries. For
the hydrogen mis-matches, you can just remove those atoms from the pdb, and
let LEaP put them in. For phosphotyrosine, you have to change the residue
name to match a residue you would read in (check the contributed parameters
database at the Amber web site). Amber thinks that TYR is ordinary tyrosine.

...good luck...dac

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