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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Received on Wed Mar 20 2013 - 11:00:02 PDT
