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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Received on Wed Oct 17 2012 - 08:30:04 PDT
