AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Sep 27 2008 - 08:46:10 CDT

Hi:
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 "prepare_amber.pl"
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?

Thanks

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