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
>
>
>
>
>
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>
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
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Received on Wed Mar 20 2013 - 11:00:03 PDT
