This has been seen before and is caused because the radius for Zn is not
defined in the sander source code. You can change it and re-compile
according to the instructions shown here:
http://structbio.vanderbilt.edu/archives/amber-archive/2009/5852.php
-Bill
On Wed, Oct 17, 2012 at 11:27 AM, Maryam Hamzehee
<maryam_h_7860.yahoo.com>wrote:
>
>
> Dear All
>
> I am trying to calculate the decomposition energy for my protein-DNA
> complex. I have two zinc in my complex and I have prepared the ZNA.lib and
> prepared the *.prmtop and *.inpcrd files successfully. When I am doing the
> calculation of binding energy it works but in the case of per residue
> decomposition energy it gives the following error:
>
>
>
>
>
> Running MMPBSA.MPI on 28 processors...
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> ptraj found! Using /share/apps/amber11/bin/ptraj
> sander found! Using /share/apps/amber11/bin/sander for GB calculations
> Preparing trajectories for simulation...
> 40 frames were read in and processed by ptraj for use in calculation.
>
> Beginning GB calculations with sander...
> calculating complex contribution...
> bad atom type: ZN
> bad atom type: ZN
> bad atom type: ZN
> bad atom type: ZN
> bad atom type: ZN
> bad atom type: ZN
> bad atom type: ZN
> bad atom type: ZN
> bad atom type: ZN
> bad atom type: ZN
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> bad atom type: ZN
> bad atom type: ZN
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
>
> .
> .
> .
> my input files are :
>
> mmpbsa_per_res_decomp.in
>
> Per-residue GB and PB decomposition
> &general
> endframe=50, verbose=1,
> /
> &gb
> igb=5, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
> &decomp
> idecomp=1, print_res="1-73"
> dec_verbose=1,
>
>
>
> the script is:
>
> decomp.pbs
>
> #PBS -lnodes=7:ppn=4
>
> cd $PBS_O_WORKDIR
>
> mpirun -np 28 --hostfile $PBS_NODEFILE $AMBERHOME/bin/MMPBSA.MPI -O -i
> mmpbsa_per_res_decomp.in -o FINAL_RESULTS_MMPBSA.dat
> -spdof1_na_solvated.prmtop -cpdof1.prmtop -rpdof1_zn.prmtop -lpdna.prmtop
> -y prod1.mdcrd > progress.log 2>&1
>
>
>
> Any help in this regard would be highly appreciated.
>
> Thanks
> Maryam
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-846-1633
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Received on Wed Oct 17 2012 - 09:00:05 PDT
