AMBER Archive (2009)

Subject: [AMBER] file contains 2 atoms not in residue templates

From: Workalemhu Berhanu (wberhanu_at_mail.ucf.edu)
Date: Sat May 23 2009 - 19:17:09 CDT

Dear all

Hello

When I was loading a pdb file with the amino acid sequence of two strands of mvggvv I got in xleap that file contains 2 atoms not in the residue template. I am using amber9. When I examined my molecule I found out there are two sulfur atoms from the methionine amino acid. Can anyone help me in fixing my problem?
Loading PDB file: ./mvggvv.pdb
Created a new atom named: OT within residue: .R<CVAL 6>
  Added missing heavy atom: .R<CVAL 6>.A<OXT 17>
Created a new atom named: OT within residue: .R<CVAL 12>
  Added missing heavy atom: .R<CVAL 12>.A<OXT 17>
  total atoms in file: 76
  Leap added 90 missing atoms according to residue templates:
       2 Heavy
       88 H / lone pairs
  The file contained 2 atoms not in residue templates

I thank you in advance

Workalemahu

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber