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
>
>_______________________________________________
>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
Received on Thu May 31 2012 - 19:30:03 PDT
