AMBER Archive (2009)

Subject: [AMBER] problem with minimization

From: moitrayee_at_mbu.iisc.ernet.in
Date: Thu Oct 22 2009 - 06:01:14 CDT

Dear Amber Users,

I want to simulate a protein-ligand-trna complex in its dimeric state. When I
prepare this pdb and subject it to leap for generation of .prmtop and .prmcrd
files, no error is shown. However, the system shows segmentation fault in
minimization step.
 Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
***** Processor 31
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
 In this slab, Atoms found: 128074 Allocated: 8538

rank 31 in job 5 compute-0-5.local_33031 caused collective abort of all ranks
  exit status of rank 31: killed by signal 9
rank 15 in job 5 compute-0-5.local_33031 caused collective abort of all ranks
  exit status of rank 15: killed by signal 9
rank 7 in job 5 compute-0-5.local_33031 caused collective abort of all ranks
  exit status of rank 7: killed by signal 9
rank 0 in job 5 compute-0-5.local_33031 caused collective abort of all ranks
  exit status of rank 0: killed by signal 9

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander.MPI 0000000000512DEF Unknown Unknown Unknown
sander.MPI 00000000006F0E54 Unknown Unknown Unknown
sander.MPI 00000000004BE957 Unknown Unknown Unknown
sander.MPI 00000000004B5AAD Unknown Unknown Unknown
sander.MPI 0000000000407B22 Unknown Unknown Unknown
libc.so.6 000000332471C3FB Unknown Unknown Unknown
sander.MPI 0000000000407A6A Unknown Unknown Unknown

To check, I have seen that the protein+trna or the protein+ligand gives no such
error in the dimeric state. Again, there is no error in the full complex in the
monomeric state. Also, to check, I have taken protein and trna from both
subunits but ligand from just one subunit and no segmentation fault is seen
during minimization. I have repeated this for both the subunits.
Please help me out with your valuable suggestions. I am attaching my complete
pdb file. I am also attaching the parameter files for the ligand.

Thanks a lot in advance.

Sincere Regards,
Moitrayee 

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