Your solvated topology file lacks any information to tell Amber that it has
a solvent box. The IFBOX variable is set to 0 (see
http://ambermd.org/formats.html), there is no BOX_DIMENSIONS,
ATOMS_PER_MOLECULE, or SOLVENT_POINTERS sections to the topology file.
Therefore, this topology file never should have worked for Amber
simulations with ntb=1 or ntb=2.
IFBOX provides information about what kind of box the system has (e.g.,
orthogonal or truncated octahedron), and therefore indicates how imaging
should be done. Since MMPBSA.py can't determine any box information from
the solvated topology file, and therefore can't determine how to image the
system, it quits with an error, since it doesn't trust the topology file.
In my experience, I've never seen a topology file created with "solvateoct"
generate a topology file with IFBOX==0, so I'm not sure how your topology
file came from the commands you gave. Did you modify your topology file in
any way? If not, can you attach the files necessary to generate your
topology file in tleap?
Thanks!
Jason
On Thu, May 31, 2012 at 8:50 PM, Cao Yang <muxiachuixue.163.com> wrote:
> Hi Jason,
>
> I have sent the solvated topology file to jason.swails.gmail.com. You
> can check it
> Thanks a lot.
>
>
>
>
>
> At 2012-06-01 11:36:26,"Jason Swails" <jason.swails.gmail.com> wrote:
> >Can you attach the solvated topology file please? IFBOX should be 2 if
> you used the solvateoct command. I am wary to trust your topology file due
> to this error.
> >
> >--
> >Jason M. Swails
> >Quantum Theory Project,
> >University of Florida
> >Ph.D. Candidate
> >352-392-4032
> >
> >On May 31, 2012, at 10:13 PM, "Cao Yang" <muxiachuixue.163.com> wrote:
> >
> >> I made my solvated topology file in the steps below:
> >>
> >> tleap -f leaprc.ff99SB
> >> source leaprc.gaff
> >> LUT=loadmol2 LUT.mol2 ## my ligand
> >> loadamberparams LUT.frcmod
> >> com=loadpdb com_nosolv.pdb
> >> charge com
> >> addions2 com Na+ 6
> >> solvateoct com TIP3PBOX 8.0
> >> saveamberparm com com_solv.prmtop com_solv.inpcrd
> >> quit
> >>
> >> The file com_solv.prmtop is the solvated complex topology file. Is
> there anything wrong with that?
> >> Thanks again.
> >>
> >>
> >>
> >>
> >>
> >> At 2012-06-01 10:02:00,"Jason Swails" <jason.swails.gmail.com> wrote:
> >>> How did you make your solvated complex topology file? Can you attach
> it to your email?
> >>>
> >>> --
> >>> Jason M. Swails
> >>> Quantum Theory Project,
> >>> University of Florida
> >>> Ph.D. Candidate
> >>> 352-392-4032
> >>>
> >>> On 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
> >>>
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> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 01 2012 - 06:00:04 PDT
