Hi,
The modifications I had suggested must NOT be made in the input file for
MMPBSA.py, but in the input files that MMPBSA.py generates for the
programs that do the energy calculations (for PB, they are called
_MMPBSA_pb.mdin).
The idea is that you run first MMPBSA.py with the '-make-mdins' option,
which will create those inputs. Then, you modify those "mdin" files as
suggested and finally, you run again MMPBSA.py with the '-use-mdins' option.
The options I suggested should work with AMBER 12 / AmberTools12.
Besides, to use non-linear PB you need sander/pbsa, whereas the default
in MMPBSA.py is, I believe, to use mmpbsa_py_energy. To force the use of
sander, you need to include the 'use_sander=1' option in the '&general'
section of your input for MMPBSA.py.
As for the best treatment of Mg2+ in your case, I think others will give
you better advice than me...
Good luck!
Miguel
Le 21/03/13 15:08, Giulia Palermo a écrit :
> Dear Dr. Miguel Ortiz Lombardía,
>
> thank you very much for your quick reply and helpful suggestions.
> However, several problems are present.
> As you suggested, the linearized PB is not suitable for my system, given the fact that the output energies are unreasonable (2000 kcal/mol)!!!!
>
> So, I moved to the non-linearized PB calculations, using the following input file:
>
> &general
> endframe=300, keep_files=2, interval=5, netcdf=1
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100, inp=1, radiopt=0,
> npbverb=1, accept=0.000001,
> use_sav=0, sprob=1.4, dprob=1.4,
> npbopt=1, eneopt=1, bcopt=5,
>
> Unfortunately, the calculation crashes with the following errors:
> InputError: Unknown variable npbverb in &pb
>
> and if I delete npbverb and other options the problem persists, as I obtain the following:
> InputError: Unknown variable use_sav in &pb
>
> I have to tell you that in my system there are six co-crystallized Mg2+ ions that are crucial for anchoring the DNA to the protein and for attaining the catalytic mechanism. Therefore, these Mg2+ can not be deleted.
>
> Do you have any idea on the solution of the problem??
>
> thank you very much in advance
> Giulia
>
>
>
>
>
> ________________________________________
> Da: Miguel Ortiz Lombardía [miguel.ortiz-lombardia.afmb.univ-mrs.fr]
> Inviato: giovedì 21 marzo 2013 11.18
> A: AMBER Mailing List
> Oggetto: Re: [AMBER] mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex
>
> Hi Giulia,
>
> You need:
>
> inp=1,
> radiopt=0,
>
> to use the radii from the prmtop file. Note that you should not use
> radiopt=0 with the inp=2 option.
>
> Also, for a highly charged system like DNA my understanding is that the
> linear approximation to the Poisson-Boltzmann equation does not hold, so
> you should use non-linear PB. To do that with MMPBSA.py you need a bit
> of hacking to modify the input files for pbsa. If you want to try, I use
> this within the shell script I run to launch the calculations:
>
>> # Create first the inputs
>> MMPBSA.py.MPI -O -i ./binding-${inprot}-${complex}.in -o ${complex}_${post}_${protocol}_mmpbsa.dat -sp ../../${tot}_${post}_sol.prmtop -cp ../../${tot}_${post}_vac.prmtop -rp ../../${rec}_${post}_vac.prmtop -lp ../../${lig}_${post}_vac.prmtop -y ../../${tot}_${post}_sol_prod${prod}_0*mdcrd -make-mdins
>> # Non-linear PBSA
>> # Add some verbosity
>> perl -pi'orig01_*' -e 's|&pb\n|&pb\n npbverb=1, accept=0.000001,\n|' _MMPBSA_${mdinprot}.mdin
>> # Make sure inp=1 related options are taken into account
>> # Change the PB solver to nonlinear because we have DNA
>> perl -pi'orig02_*' -e 's|&pb\n|&pb\n use_sav=0, sprob=1.4, dprob=1.4,\n npbopt=1, eneopt=1, bcopt=5,
>> # RUN
>> MMPBSA.py.MPI -i ./binding-${inprot}-${complex}.in -o ${complex}_${post}_${protocol}_mmpbsa.dat -eo ${complex}_${post}_${protocol}_mmpbsa -sp ../../${tot}_${post}_sol.prmtop -cp ../../${tot}_${post}_vac.prmtop -rp ../../${rec}_${post}_vac.prmtop -lp ../../${lig}_${post}_vac.prmtop -y ../../${tot}_${post}_sol_prod${prod}_0*mdcrd -use-mdins
>
> You need of course to substitute the shell variables for whatever fits
> your files.
>
> Cheers,
>
> --
> Miguel Ortiz Lombardía
>
> Architecture et Fonction des Macromolécules Biologiques (UMR7257)
> CNRS, Aix-Marseille Université
> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
> Tel: +33(0) 491 82 55 93
> Fax: +33(0) 491 26 67 20
> mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
> http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
>
> Le 21/03/13 10:14, Giulia a écrit :
>> Dear Dr. Miguel Ortiz Lombardía,
>>
>> I changed the default value in the mmpbsa.in from inp=2 to inp=1.
>> GB calculations are going well.
>> However, the problem with the radius assigned to the 38 CG2 C3 atom persists in PB calculations.
>> Indeed, I have the same error.
>>
>> CalcError: /softmp/AMBER12/amber12/bin/mmpbsa_py_energy failed with prmtop Complex.prmtop!
>> PB Bomb in pb_aaradi(): No radius assigned for atom 38 CG2 C3
>>
>>
>> there is a way to define this radius and avoid the problem?
>> Or an other way to skip it??
>>
>>
>> Thank you very much
>> Giulia Palermo
>>
>>
>> Il giorno 20/mar/2013, alle ore 18.52, Miguel Ortiz Lombardia ha scritto:
>>
>>> El 20/03/13 18:33, Giulia Palermo escribió:
>>>> Dear all,
>>>>
>>>> I am running some MMPBSA post-processing calculations on a ternary system composed by PROTEIN, DNA and a LIGAND intercalating the dna.
>>>> I am considering the protein/dna complex as the RECEPTOR, whereas the intercalating ligand is (effectively) the LIGAND.
>>>> A total of 60 frames is processed on 12 processors (5 frames per processor).
>>>>
>>>> In the mmpbsa.in (input) file, I am asking for both GB (first calculation) and PB (second calculations).
>>>> However, calculations are crashing after processing only one frame.
>>>>
>>>> In the "_MMPBSA_receptor_gb.mdout" file, I found the following:
>>>>
>>>> bad number of bonds to C: 37 1; using default carbon parameters
>>>> bad number of bonds to C: 323 1; using default carbon parameters
>>>> ...etc...
>>>> Using carbon SA parms for atom type MG
>>>> Using carbon SA parms for atom type MG
>>>> ...etc...
>>>>
>>>> Moreover, when the calculation crashes, I have the message on the bottom.
>>>> It seems that an error is present in the Complex.prmtop! file
>>>> However, I have prepared this file using the same procedure that I used for generating the original topologies (using tleap).
>>>>
>>>> Do you have any idea on how to solve the problem???
>>>> Thank you very much for your help.
>>>>
>>>> Giulia Palermo
>>>>
>>>> mmpbsa_py_energy found! Using /softmp/AMBER12/amber12/bin/mmpbsa_py_energy
>>>> cpptraj found! Using /softmp/AMBER12/amber12/bin/cpptraj
>>>> Preparing trajectories for simulation...
>>>> 60 frames were processed by cpptraj for use in calculation.
>>>>
>>>> Beginning GB calculations with /softmp/AMBER12/amber12/bin/mmpbsa_py_energy
>>>> calculating complex contribution...
>>>> calculating receptor contribution...
>>>> calculating ligand contribution...
>>>>
>>>> Beginning PB calculations with /softmp/AMBER12/amber12/bin/mmpbsa_py_energy
>>>> calculating complex contribution...
>>>> CalcError: /softmp/AMBER12/amber12/bin/mmpbsa_py_energy failed with prmtop
>>>> Complex.prmtop!
>>>> PB Bomb in pb_aaradi(): No radius assigned for atom 38 CG2 C3
>>>>
>>>> Error occured on rank 5.
>>>> Exiting. All files have been retained.
>>>> --------------------------------------------------------------------------
>>>> MPI_ABORT was invoked on rank 5 in communicator MPI_COMM_WORLD
>>>> with errorcode 1.
>>>>
>>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>>> You may or may not see output from other processes, depending on
>>>> exactly when Open MPI kills them.
>>>> --------------------------------------------------------------------------
>>>> CalcError: /softmp/AMBER12/amber12/bin/mmpbsa_py_energy failed with prmtop
>>>> Complex.prmtop!
>>>> PB Bomb in pb_aaradi(): No radius assigned for atom 38 CG2 C3
>>>>
>>>> Error occured on rank 7.
>>>> Exiting. All files have been retained.
>>>> --------------------------------------------------------------------------
>>>> mpirun has exited due to process rank 5 with PID 12808 on
>>>> node koseidon exiting improperly. There are two reasons this could occur:
>>>>
>>>> 1. this process did not call "init" before exiting, but others in
>>>> the job did. This can cause a job to hang indefinitely while it waits
>>>> for all processes to call "init". By rule, if one process calls "init",
>>>> then ALL processes must call "init" prior to termination.
>>>>
>>>> 2. this process called "init", but exited without calling "finalize".
>>>> By rule, all processes that call "init" MUST call "finalize" prior to
>>>> exiting or it will be considered an "abnormal termination"
>>>>
>>>> This may have caused other processes in the application to be
>>>> terminated by signals sent by mpirun (as reported here).
>>>> --------------------------------------------------------------------------
>>>> [koseidon:12801] 1 more process has sent help message help-mpi-api.txt / mpi-abort
>>>> [koseidon:12801] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
>>>>
>>>> [1] Exit 1 /softmp/AMBER12/amber12/bin/mpirun -np 12 /softmp/AMBER12/amber12/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp Complex.prmtop! -rp prot_dna.prmtop -lp lig.prmtop -y traj.mdcrd
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>> Hi Giulia,
>>>
>>> Have you used the ff10 force field? If so, you cannot use the inp=2
>>> option with pbsa, some atoms are not properly processed with this option
>>> and you need to go for inp=1. Make sure you have patched your AMBER
>>> 12/AmberTools12 installation. Also, check carefully that the defaults
>>> you are using in the calculations correspond to those needed for inp=1.
>>>
>>> Cheers,
>>>
>>> --
>>> Miguel Ortiz Lombardía
>>>
>>> Architecture et Fonction des Macromolécules Biologiques (UMR7257)
>>> CNRS, Aix-Marseille Université
>>> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
>>> Tel: +33(0) 491 82 55 93
>>> Fax: +33(0) 491 26 67 20
>>> mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
>>> http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
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>>
>
>
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>
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>
--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
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Received on Thu Mar 21 2013 - 08:00:04 PDT
