This is an error check that was added after AmberTools 1.5 was released,
which is why it isn't caught with AmberTools 1.5. This check is to prevent
users from specifying a topology file as the solvated complex topology file
if no box information is present in the prmtop. If the topology file was
used for solvated MD, then it should have box information (i.e. IFBOX not
equal to 0). In other words, something seems incorrect about your solvated
complex topology file because it does not have information bout the
periodic box.
I hope that helps.
-Bill
On Thu, May 31, 2012 at 9:05 PM, Cao Yang <muxiachuixue.163.com> wrote:
> Thanks for your reply. My command line is as below:
> mpirun -np 12 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
> -sp com_solv.prmtop -cp com_nosolv.prmtop -rp rec.prmtop -lp
> neg_gaussian_LUT.prmtop -y ../production2.mdcrd > progress.log 2>&1
>
> When I use the same command line to run the job with AmberTools 1.5, the
> calculation ended smoothly. Is there anything difference in preparing the
> input file and topology files between AmberTools 1.5 and AmberTools 12 ?
>
>
>
>
> At 2012-06-01 01:20:26,"Bill Miller III" <brmilleriii.gmail.com> wrote:
> >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
> >> _______________________________________________
> >> AMBER mailing list
> >> 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
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> 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 - 19:00:04 PDT
