AMBER: abnormal termination of tleap

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

Hi Amber Community,

Greetings.

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
!
!ABORTING.

*********************************

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

Thanks and Regards

Pankaj


===================================================================
If your ship doesn't come in, swim out to it.......Jonathan Winters
===================================================================
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |
===================================================================


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Mar 11 2007 - 06:07:32 PDT
Custom Search