If you google for the the error 'bad atom type: F' you will find quite a
few responses from the Amber list, such as
http://archive.ambermd.org/201201/0129.html. You will likely need to find
the appropriate section in mdread.f that applies to where the decomposition
analysis is being performed (note that multiple locations in mdread.f
involve the reading of atomic information, and you need to make sure to
modify the section that corresponds to your calculation type) and add in
the F radius information. Make sure to re-compile sander after you make the
change.
-Bill
On Tue, Aug 13, 2013 at 10:45 AM, Kshatresh Dutta Dubey <kshatresh.gmail.com
> wrote:
> Dear Users,
>
> I am using MMPBSA.py (AmberTools 13) for energy decomposition. The same
> complex topology runs fine for binding energy and nmode analysis while it
> is showing error like-
>
> *bash: module: line 1: syntax error: unexpected end of file*
> *bash: error importing function definition for `module'*
> * bad atom type: F*
> * bad atom type: F*
> * bad atom type: F*
> * bad atom type: F*
> * bad atom type: F*
>
> *--------------------------------------------------------------------------*
> *MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD*
> *with errorcode 1.*
> *
> *
> *NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.*
> *You may or may not see output from other processes, depending on*
> *exactly when Open MPI kills them.*
>
> *--------------------------------------------------------------------------*
> *CalcError: /home/kshatresh/amber12/bin/sander failed with prmtop
> ../complex.top!*
> *Error occured on rank 8.*
> *Exiting. All files have been retained.*
> *CalcError: /home/kshatresh/amber12/bin/sander failed with prmtop
> ../complex.top!*
> *Error occured on rank 0.*
> *Exiting. All files have been retained.*
> *CalcError: /home/kshatresh/amber12/bin/sander failed with prmtop
> ../complex.top!*
> *Error occured on rank 2.*
> *
> *
> I wonder why same complex topology file is working fine for binding energy
> and NMODE analysis while not working for decomposition analysis.
> Please help me to point out the problem.
> Thanks in advance
> --
> With best regards
>
> ****************************************************************************************************************
> Dr. Kshatresh Dutta Dubey
> Post Doctoral Fellow
> Indian Institute of Technology Kanpur
> Kanpur, India
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D.
352-846-1633
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Received on Tue Aug 13 2013 - 21:00:02 PDT
