AMBER Archive (2008)

Subject: AMBER: Leap atoms CL and OXT do not have a type

From: Francesco Pietra (
Date: Sat Sep 27 2008 - 08:46:10 CDT

I have a problematic pdb file for leap (or for me!). It is for a
multimer created with Modeller and contains chloride ions ligands.

Before MD with Amber I attempted docking of both polypeptides (DOT2)
and small molecules (DOCK6.2). The first ones successful, the second
ones unsuccessful at the Amber score stage. Command ""
did not recognize the CL residue (which is a problem that I'll discuss
at dock-fans)

Therefore, I made recourse to leap (Amber10, Amber tools 1.0), loading
"leaprc.ff99SB" and "leaprc.gaff" only. This resulted in a couple of
errors for each chain for failure to deal with "atom named OXT" and
"residue CL".

>From leap.log for the first chain:

Unknown residue: CL number: 420 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck

Created a new atom named: OXT within residue: .R<LYS 420>
Creating new UNIT for residue: CL sequence: 421
One sided connection. Residue: missing connect0 atom.
Creating a new atom named: CL within residue: .R<CL 421>

Similarly for the other chains. Finally

WARNING: The unperturbed charge of the unit: -47.000000 is not zero.
FATAL: Atom .R<LYS 420>.A<OXT 23> does not have a type.

Similarly for the other chains.

Does that suggest that I must load some other files into leap besides
ff99SB and gaff, or other changes are suggested by the OXT issue?


francesco pietra
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)