AMBER Archive (2006)

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

From: bertrand russell (betrussell23_at_gmail.com)
Date: Thu Dec 07 2006 - 04:39:46 CST

Hello Case,

                  Thank you very much for your kind suggestion. I followed
your suggestion and corrected the FATALs concerning with NMET. Unfortunately
I couldn't correct the FATAL errors for the added Phosphate group. I made
changes is the input PDB file in reference to the contributed database
entry. Eventhen, it is not recognising the atom types. I even tried adding
the entry to the all_amino94.lib file which is in the leap's dat directory.
But it is not recognising the Phosphorylated TYR residue. Do I need to add
the entry and recompile my AMBER9 again? Waiting for your suggestions. 

-- 
Live Life; Don't pass it
Bertrand.P.S.Russell

On 12/2/06, David A. Case <case_at_scripps.edu> wrote:
>
> 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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-- 
Live Life; Don't pass it
Bertrand.P.S.Russell

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