AMBER Archive (2006)

Subject: AMBER: LEaP not recognising Phosphate group in TYR

From: bertrand russell (betrussell23_at_gmail.com)
Date: Sat Dec 02 2006 - 10:41:23 CST

Dear Amber users,

                              I am a new user of amber. When I tried to load
my pdb file to which I added phophate groups using INSIGHT 2 builder module,
I am getting the following fatal errors. One thing I could not understand
is,
FATAL: Atom .R<NMET 1>.A<H 20> does not have a type.
When I used the same file without the addition of phophate groups to the TYR
residues I am not getting this particular error message. Thanks for your
help.

Checking Unit.
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.
FATAL: Atom .R<TYR 189>.A<OP2 26> does not have a type.
FATAL: Atom .R<TYR 189>.A<OP3 27> does not have a type.
FATAL: Atom .R<TYR 189>.A<OP4 28> does not have a type.
FATAL: Atom .R<TYR 193>.A<HB1 22> does not have a type.
FATAL: Atom .R<TYR 193>.A<HZ 23> does not have a type.
FATAL: Atom .R<TYR 193>.A<P 24> does not have a type.
FATAL: Atom .R<TYR 193>.A<OP1 25> does not have a type.
FATAL: Atom .R<TYR 193>.A<OP2 26> does not have a type.
FATAL: Atom .R<TYR 193>.A<OP3 27> does not have a type.
FATAL: Atom .R<TYR 193>.A<OP4 28> does not have a type.
FATAL: Atom .R<TYR 194>.A<HB1 22> does not have a type.
FATAL: Atom .R<TYR 194>.A<P 23> does not have a type.
FATAL: Atom .R<TYR 194>.A<OP1 24> does not have a type.
FATAL: Atom .R<TYR 194>.A<OP2 25> does not have a type.
FATAL: Atom .R<TYR 194>.A<OP3 26> does not have a type.
FATAL: Atom .R<TYR 194>.A<OP4 27> does not have a type.
Failed to generate parameters
Parameter file was not saved. 

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

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