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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 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 > > > _______________________________________________ > 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/amberReceived on Thu Mar 21 2013 - 07:30:02 PDT