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 > > > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber_at_scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >

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

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