AMBER: Problem with xleap

From: Ilyas Yildirim <>
Date: Wed, 11 May 2005 21:45:50 -0400 (EDT)

Dear All,

I have a question regarding xleap. It is about the AMBER's libraries, and
something strange is happening when I am trying to do the following:

I start 'xleap'. Then;

> source leaprc.ff99
> savepdb RC rc.pdb
> quit

Now, I see the file 'rc.pdb' in the directory. Then I start 'xleap' again;

> source leaprc.ff99
> molecule = loadpdb rc.pdb

and xleap adds 2 atoms!!! Here is what xleap is giving me after I load the

> molecule = loadpdb rc.pdb
Loading PDB file: ./rc.pdb
Created a new atom named: O2* within residue: .R<RC 1>
Created a new atom named: HO*2 within residue: .R<RC 1>
  Added missing heavy atom: .R<RC 1>.A<O2' 29>
  total atoms in file: 31
  Leap added 2 missing atoms according to residue templates:
       1 Heavy
       1 H / lone pairs
  The file contained 2 atoms not in residue templates
  Since added/missing = extra, there is a high probability
  of atoms with 'incorrect' names; you may want to
  use addPdbAtomMap to map these names, or change in file

Question: I have saved the .pdb structure according to the AMBER' residue
library, and when I try to open the same .pdb in xleap, it adds two atoms
(saying that they are missing, even though they are not!). Am I missing
something here? Thanks in advance for your responses.


  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu May 12 2005 - 03:52:59 PDT
Custom Search