Dear Cuiyl
Even i was facing the similar problem and this why the error has occured,
This error has occured because there is no Atomic radii of Fe in the
mdread.f file and you need to add the radius of Fe in that and you will
require to re-install Amber again after adding the atomic radius of Fe.
*Thanks & Regards*
*
*
*Siddharth S . kesharwani
M.S.(Pharm.) Scholar
Department of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research (NIPER)
Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
Mob. 09646948577*
On Thu, Mar 14, 2013 at 10:33 AM, Cuiyl <cuiyinglukitty.gmail.com> wrote:
> Dear all amber users:
>
> I've been simulating a protein system containing Fe atoms. The
> Fe atoms are bound to residues in the protein. I am trying to do an
> MMPBSA calculation on my protein complex. Previous MMPBSA caIculations
> of PB/GB and entropy ended normally. But when I try to do an energy
> decomposition I get an the error:
>
> "bad atom type: fe
> bad atom type: fe
> bad atom type: fe
> bad atom type: fe
> bad atom type: fe
> bad atom type: fe
> bad atom type: fe
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor"
>
> I've check the mm_pbsa_calceneent.pm file, it includes a parameter line
> for FE.
> "FE" => 1.300 + 1.400,
> Any ideas of how to overcome this problem?
>
> Thanks,
> Cuiyl
>
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Received on Wed Mar 13 2013 - 23:30:02 PDT
