AMBER: abnormal termination of tleap

From: Pankaj R. Daga <>
Date: Fri, 9 Mar 2007 16:24:37 -0600

Hi Amber Community,


I am trying to set-up one protein-ligand complex with the help of tleap. The protein, which I am dealing with is a homology modeled metalloprotein containing Mg+2 and the ligand is nucleotide.

While loading pdb in tleap, I encountered one error and abnormal termination of tleap. The error is mentioned below


  Added missing heavy atom: .R<DG3 392>.A<O3' 33>
  Added missing heavy atom: .R<CTP 393>.A<P1 2>
One sided connection. Residue: MG2 missing connect0 atom.
Bond: maximum coordination exceeded on .R<CTP 393>.A<P323 7>
      -- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R<CTP 393>.A<P323 7> .R<CTP 393>.A<O1G 1>
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 444
!FATAL: Message: bondAtomProblem found


Could you please suggest me, the solution for this problem?

Thanks and Regards


If your ship doesn't come in, swim out to it.......Jonathan Winters
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail:
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |
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Received on Sun Mar 11 2007 - 06:07:32 PDT
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