AMBER Archive (2004)

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

From: Rhonda Torres (
Date: Sun Feb 22 2004 - 16:23:59 CST

Hi Scopio,

To help you build a *.lib file, you should look at the plastocyanin

This will get you started. We are in the process of updating this
tutorial and the new page should be up soon, however, this shows how to
make a *.lib (or as named in the tutorial for the modified HIS and MET
residues, *.in). One thing the current page doesn't state is that you
need to addAtomTypes for your "new" atoms (the new page states this). As
an example:

addAtomTypes {
  {"SM" "S" "sp3"}

needs to be included in your xleap commands to recognize the SM atom type
that was created for the modified MET residue (

Hope this helps.


Rhonda A. Torres
The Scripps Research Institute
Department of Molecular Biology
10550 N. Torrey Pines Rd. TPC 15
La Jolla, CA 92037

phone: (858) 784-9781
fax: (858) 784-8896

On Sun, 22 Feb 2004, scopio wrote:

> 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!
> scopio

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