Hi Jason,
I must say I made a big mistake. I modified one of the crystal water's name from WAT to H2O in com_solv.pdb and saved a new
topology file named com_solv.prmtop. This action loses the box information although the water molecules are still there.
Thanks for your patience again. I apologize for my carelessness.
Cao Yang,
Zhejiang Unieversity
At 2012-06-01 20:51:01,"Jason Swails" <jason.swails.gmail.com> wrote:
>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
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>
>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Jun 01 2012 - 06:30:02 PDT
