AMBER Archive (2006)

Subject: AMBER: LEaP problem

From: bertrand russell (betrussell23_at_gmail.com)
Date: Mon Dec 11 2006 - 23:10:48 CST

Hai all,

                  I am Bertrand Russell, graduate student from Indian
Institute of Technology, Madras. The problem is with my phosphorylated TYR
residues in my protein, which are not recognised by LEaP program. The TYR
residues were phosphorylated by INSIGHT 2 using its builder module. LEaP is
not recognising the phosphorylated TYR residues. I posted a query in Amber
archive and got reply from Mr.D.A.Case. He suggested me to look at the
contributed parameters in the amber.scripps.edu site. I made changes in the
atom types in reference with the contributed parameers, eventhen I am
getting the errors. The error message is as follows,

FATAL: Atom .R<Y2P 189>.A<N 1> does not have a type.
FATAL: Atom .R<Y2P 189>.A<CA 2> does not have a type.
FATAL: Atom .R<Y2P 189>.A<CB 3> does not have a type.
FATAL: Atom .R<Y2P 189>.A<CG 4> does not have a type.
FATAL: Atom .R<Y2P 189>.A<CD1 5> does not have a type.
FATAL: Atom .R<Y2P 189>.A<CE1 6> does not have a type.
FATAL: Atom .R<Y2P 189>.A<CZ 7> does not have a type.
FATAL: Atom .R<Y2P 189>.A<CE2 8> does not have a type.
FATAL: Atom .R<Y2P 189>.A<CD2 9> does not have a type.
FATAL: Atom .R<Y2P 189>.A<C 10> does not have a type.
FATAL: Atom .R<Y2P 189>.A<O 11> does not have a type.
FATAL: Atom .R<Y2P 189>.A<H 12> does not have a type.
FATAL: Atom .R<Y2P 189>.A<HA 13> does not have a type.
FATAL: Atom .R<Y2P 189>.A<HB2 14> does not have a type.
FATAL: Atom .R<Y2P 189>.A<HB3 15> does not have a type.
FATAL: Atom .R<Y2P 189>.A<HD1 16> does not have a type.
FATAL: Atom .R<Y2P 189>.A<HE1 17> does not have a type.
FATAL: Atom .R<Y2P 189>.A<HE2 18> does not have a type.
FATAL: Atom .R<Y2P 189>.A<HD2 19> does not have a type.
FATAL: Atom .R<Y2P 189>.A<OG 20> does not have a type.
FATAL: Atom .R<Y2P 189>.A<P 21> does not have a type.
FATAL: Atom .R<Y2P 189>.A<O1P 22> does not have a type.
FATAL: Atom .R<Y2P 189>.A<O2P 23> does not have a type.
FATAL: Atom .R<Y2P 189>.A<O3P 24> does not have a type.
FATAL: Atom .R<Y2P 193>.A<N 1> does not have a type.
FATAL: Atom .R<Y2P 193>.A<CA 2> does not have a type.
FATAL: Atom .R<Y2P 193>.A<CB 3> does not have a type.
FATAL: Atom .R<Y2P 193>.A<CG 4> does not have a type.
FATAL: Atom .R<Y2P 193>.A<CD1 5> does not have a type.
FATAL: Atom .R<Y2P 193>.A<CE1 6> does not have a type.
FATAL: Atom .R<Y2P 193>.A<CZ 7> does not have a type.
FATAL: Atom .R<Y2P 193>.A<CE2 8> does not have a type.
FATAL: Atom .R<Y2P 193>.A<CD2 9> does not have a type.
FATAL: Atom .R<Y2P 193>.A<C 10> does not have a type.
FATAL: Atom .R<Y2P 193>.A<O 11> does not have a type.
FATAL: Atom .R<Y2P 193>.A<H 12> does not have a type.
FATAL: Atom .R<Y2P 193>.A<HA 13> does not have a type.
FATAL: Atom .R<Y2P 193>.A<HB2 14> does not have a type.
FATAL: Atom .R<Y2P 193>.A<HB3 15> does not have a type.
FATAL: Atom .R<Y2P 193>.A<HD1 16> does not have a type.
FATAL: Atom .R<Y2P 193>.A<HE1 17> does not have a type.
FATAL: Atom .R<Y2P 193>.A<HE2 18> does not have a type.
FATAL: Atom .R<Y2P 193>.A<HD2 19> does not have a type.
FATAL: Atom .R<Y2P 193>.A<OG 20> does not have a type.
FATAL: Atom .R<Y2P 193>.A<P 21> does not have a type.
FATAL: Atom .R<Y2P 193>.A<O1P 22> does not have a type.
FATAL: Atom .R<Y2P 193>.A<O2P 23> does not have a type.
FATAL: Atom .R<Y2P 193>.A<O3P 24> does not have a type.
FATAL: Atom .R<Y2P 194>.A<N 1> does not have a type.
FATAL: Atom .R<Y2P 194>.A<CA 2> does not have a type.
FATAL: Atom .R<Y2P 194>.A<CB 3> does not have a type.
FATAL: Atom .R<Y2P 194>.A<CG 4> does not have a type.
FATAL: Atom .R<Y2P 194>.A<CD1 5> does not have a type.
FATAL: Atom .R<Y2P 194>.A<CE1 6> does not have a type.
FATAL: Atom .R<Y2P 194>.A<CZ 7> does not have a type.
FATAL: Atom .R<Y2P 194>.A<CE2 8> does not have a type.
FATAL: Atom .R<Y2P 194>.A<CD2 9> does not have a type.
FATAL: Atom .R<Y2P 194>.A<C 10> does not have a type.
FATAL: Atom .R<Y2P 194>.A<O 11> does not have a type.
FATAL: Atom .R<Y2P 194>.A<H 12> does not have a type.
FATAL: Atom .R<Y2P 194>.A<HA 13> does not have a type.
FATAL: Atom .R<Y2P 194>.A<HB2 14> does not have a type.
FATAL: Atom .R<Y2P 194>.A<HB3 15> does not have a type.
FATAL: Atom .R<Y2P 194>.A<HD1 16> does not have a type.
FATAL: Atom .R<Y2P 194>.A<HE1 17> does not have a type.
FATAL: Atom .R<Y2P 194>.A<HE2 18> does not have a type.
FATAL: Atom .R<Y2P 194>.A<HD2 19> does not have a type.
FATAL: Atom .R<Y2P 194>.A<OG 20> does not have a type.
FATAL: Atom .R<Y2P 194>.A<P 21> does not have a type.
FATAL: Atom .R<Y2P 194>.A<O1P 22> does not have a type.
FATAL: Atom .R<Y2P 194>.A<O2P 23> does not have a type.
FATAL: Atom .R<Y2P 194>.A<O3P 24> does not have a type.
Failed to generate parameters
Parameter file was not saved.
> quit
        Quit

Could anyone suggest me to correct these FATALs? Do I need to add the entry
for Phosphorylated TYR (Y2P) to my LEaP's library file and recompile the
AMBER9 again? Thanks in advance. 

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

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