Dear amber users,
It is my first time to use Nmode to calculate entropy.
I have met with two problems:
1. I extracted 10 snapshots to do the calculation and the system is a protein and ligand complex with 10550 atoms. It seems extreme time consuming. I submit the mpi job with 8 threads and it keep running for more than one week. And the job is still running. Is this normal for the calculation? There are no error output informed. How long will it take for a system like that?
2. I tried to use 5 snapshots to do the calculation. The job quitted abnormally.
The output file is:
Running MMPBSA.MPI on 4 processors...
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home/rkong/amber11/bin/ptraj
nmode program found! Using /home/rkong/amber11/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
1000 frames were read in and processed by ptraj for use in calculation.
Beginning nmode calculations with mmpbsa_py_nabnmode...
Master thread is calculating normal modes for 2 frames
calculating complex contribution for frame 0
FATAL: allocation failure in vector()
FATAL: allocation failure in vector()
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
FATAL: allocation failure in vector()
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
FATAL: allocation failure in vector()
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
The input file for 10 snapshots is as following:
&general
startframe=1,endframe=1000
keep_files=2,
receptor_mask=':1-692',ligand_mask=':693'
/
&nmode
nmstartframe=100, nmendframe=1000,
nminterval=100, nmode_igb=1, nmode_istrng=0.1,
/
The input file for 5 snapshots is as following:
&general
startframe=1,endframe=1000
keep_files=2,
receptor_mask=':1-692',ligand_mask=':693'
/
&nmode
nmstartframe=100, nmendframe=1000,
nminterval=200, nmode_igb=1, nmode_istrng=0.1,
/
The only difference between the input files is "nminterval". I just don't know why the 5 snapshots job cannot run normally as the 10 snapshots job.
Could anyone give some comments?
Best,
Ren Kong Ph.D.
Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list seven years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at methodisthealth.com. Follow us at twitter.com/MethodistHosp and www.facebook.com/MethodistHospital. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
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Received on Thu Aug 09 2012 - 10:00:05 PDT
