AMBER Archive (2009)

Subject: [AMBER] About the "FATAL: Atom err"!

From: Aurum Bai (javacfish_at_yahoo.com.cn)
Date: Mon Jun 22 2009 - 05:14:20 CDT

Hello, everyone!

I follow the protocol "http://ringo.ams.sunysb.edu/index.php/AMBER_tutorial"

When do the "check oxy" procedure, some err happy as below:

> check oxy
Checking 'oxy'....
WARNING: The unperturbed charge of the unit: 3.000000 is not zero.
FATAL: Atom .R<PTR 683>.A<N 1> does not have a type.
FATAL: Atom .R<PTR 683>.A<CA 2> does not have a type.
FATAL: Atom .R<PTR 683>.A<C 3> does not have a type.
FATAL: Atom .R<PTR 683>.A<O 4> does not have a type.
FATAL: Atom .R<PTR 683>.A<CB 5> does not have a type.
FATAL: Atom .R<PTR 683>.A<CG 6> does not have a type.
FATAL: Atom .R<PTR 683>.A<CD1 7> does not have a type.
FATAL: Atom .R<PTR 683>.A<CD2 8> does not have a type.
FATAL: Atom .R<PTR 683>.A<CE1 9> does not have a type.
FATAL: Atom .R<PTR 683>.A<CE2 10> does not have a type.
FATAL: Atom .R<PTR 683>.A<CZ 11> does not have a type.
FATAL: Atom .R<PTR 683>.A<OH 12> does not have a type.
FATAL: Atom .R<PTR 683>.A<O1P 13> does not have a type.
FATAL: Atom .R<PTR 683>.A<O2P 14> does not have a type.
FATAL: Atom .R<PTR 683>.A<O3P 15> does not have a type.
FATAL: Atom .R<PTR 683>.A<P 16> does not have a type.

Why it happen this err? who can help me?

Thank you
Aurum

      

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