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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Received on Sun Dec 03 2006 - 06:08:09 PST
