What is your command line argument to run MMPBSA.py?
The error means that MMPBSA.py is looking for solvent box information in
the solvated topology files, but could not find it. This means that the
solvated topology file (using the -sp flag) you provided did not have
information about the periodic box. If you want MMPBSA.py to strip out the
water molecules from a solvated topology file then you will need to provide
a topology file that has this box information.
-Bill
On Thu, May 31, 2012 at 1:02 PM, Cao Yang <muxiachuixue.163.com> wrote:
> Hi all,
>
> I installed AmberTools 12 resently and combine it with Amber11 by the
> following command:
> export PATH=”$AMBERHOME/bin:/home/myname/amber11/bin:$PATH”
> I ran entropy and decompsition calculation with MMPBSA.py.MPI ( or
> MMPBSA.py ) in AmberTools 12, but MMPBSA aborted with the error below:
>
> Running MMPBSA.MPI on 12 processors
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> cpptraj found! Using /home/Amber/amber12/bin/cpptraj
> mmpbsa_py_nabnmode found! Using /home/Amber/amber12/bin/mmpbsa_py_nabnmode
> Preparing trajectories for simulation...
> TrajError: Solvated topology 0 has IFBOX == 0
> Error occured on rank 0.
> Exiting. All files have been retained.
>
> I am pretty sure that the prmtop files are nothing improper because when I
> submit the same task to AmberTools 1.5 , the job completes normally.
>
> I installed AmberTools 12 in the following steps. Maybe this is something
> wrong with the installation.
> tar jxvf AmberTools12.tar.bz2
> export AMBERHOME=/home/Amber_I/amber12
> cd /home/Amber_I/amber12
> patch -p0 -N < bugfix.all ### from bugfix.1 to bugfix.7
> ./configure -nofftw3 gnu
> make install
> ./configure -mpi gnu
> make install
>
> Here is my input file:
>
> Per-residue GB and PB decomposition
> &general
> startframe=201, verbose=1,
> strip_mask=":WAT:Cl-:CIO:Cs+:IB:K+:Li+:Na+:Rb+"
> /
> &gb
> igb=5, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
> &decomp
> idecomp=1,
> dec_verbose=1,
> /
> Anyone who can give me some suggestion about this error in AmberTools 12 ?
> Many Thanks!
>
> Cao Yang,
> Zhejiang University
> _______________________________________________
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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
352-392-6715
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Received on Thu May 31 2012 - 10:30:03 PDT
