AMBER Archive (2004)

Subject: AMBER: xleap don't recognize my residue/atom

From: scopio (
Date: Sun Feb 22 2004 - 05:18:42 CST

Hi there:

I'm new to amber, I don't know how to do when xleap don't recognize
residue/atom in my pdb file.

I have a PDB file named bcl.pdb contains many atoms with several
residues. When I check pdb with 'check' command after load this pdb, the
error message occured and showed xleap couldn't recognize the types of
atoms and residues.
=======error msg=====
> check bcl
Checking 'bcl'....
FATAL: Atom .R<BCL 601>.A<MG 1> does not have a type.
FATAL: Atom .R<BCL 601>.A<CHA 2> does not have a type.
FATAL: Atom .R<BCL 601>.A<CHB 3> does not have a type.
FATAL: Atom .R<BCL 601>.A<CHC 4> does not have a type.

I searched many documents and found the problem could be resolved by
1). load a *.off/*.lib file at the start up of xleap
2). use addpdbatommap command to correct the atom names
3). use Unit Editor in xleap to creat a new unit by filling in the atom
types etc.

But none of these 3 methods could be operated for the lack of
information like below
1) how to build an off file ?
2) what atom/residue name I should map to ?
3) what atom types I should fill in ?

Looking forward to your suggestion!


  • chemical/x-pdb attachment: bcl.pdb

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