Dear amber users,
All the time I run MMPBSA on my private computer, but this time I try to use cluster. But it does not work. I have modified my input file based on the tutorial. But it still does not work. Can anyone here help me?
Input file:
MMPBSA input file to run gb
&general
startframe=50, endframe=100, interval=10, verbose=0,
ligand_mask=':421-432', receptor_mask=':1-210:211-420',
initial_traj=1, mpi_cmd='mpirun -np 4', nproc=4,
/
&gb
saltcon=0.1, igb=5,
/
&pb
/
Errors:
r.yu.euphoria:~/gid-d4-amber10$ mpirun -np 4 MMPBSA.py -i mmpbsa.in -sp complex_solvated.prmtop -cp complex.prmtop -rp re.prmtop -lp lig.prmtop -y complex_md2.mdcrd
ptraj found! Using /home/ryu/amber10/bin/ptraj
sander.MPI found! Using /home/ryu/amber10/bin/sander.MPI
ptraj found! Using /home/ryu/amber10/bin/ptraj
sander.MPI found! Using /home/ryu/amber10/bin/sander.MPI
ptraj found! Using /home/ryu/amber10/bin/ptraj
sander.MPI found! Using /home/ryu/amber10/bin/sander.MPI
ptraj found! Using /home/ryu/amber10/bin/ptraj
sander.MPI found! Using /home/ryu/amber10/bin/sander.MPI
Preparing trajectories with ptraj...
Preparing trajectories with ptraj...
Preparing trajectories with ptraj...
Preparing trajectories with ptraj...
6 frames were read in and processed by ptraj for use in calculation.
Starting sander calls
Starting gb calculation...
Error! Ptraj failed. Check coordinate and topology files for the complex.
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
Error! Ptraj failed. Check coordinate and topology files for the complex.
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
Error! Ptraj failed. Check coordinate and topology files for the complex.
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
mdfil: Error unknown flag: -y
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip rstdip -mdip mddip -ng numgroup -remlog rem.log -remtype rem.type -rem [0|1|2] -rremd [0|1|2|3] -saveene saveene -clusterinfo cluster.info -reservoir reserv/frame -hybridtraj hybrid.strip.crd-ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo -radii radii]
Consult the manual for additional options.
[euphoria.imb.uq.edu.au:26298] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1
mdfil: Error unknown flag: -y
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip rstdip -mdip mddip -ng numgroup -remlog rem.log -remtype rem.type -rem [0|1|2] -rremd [0|1|2|3] -saveene saveene -clusterinfo cluster.info -reservoir reserv/frame -hybridtraj hybrid.strip.crd-ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo -radii radii]
Consult the manual for additional options.
[euphoria.imb.uq.edu.au:26300] MPI_ABORT invoked on rank 2 in communicator MPI_COMM_WORLD with errorcode 1
mpirun noticed that job rank 1 with PID 26299 on node euphoria.imb.uq.edu.au exited on signal 15 (Terminated).
1 additional process aborted (not shown)
mdfil: Error unknown flag: -y
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo -radii radii]
Consult the manual for additional options.
Starting pb calculation...
mdfil: Error unknown flag: -y
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip rstdip -mdip mddip -ng numgroup -remlog rem.log -remtype rem.type -rem [0|1|2] -rremd [0|1|2|3] -saveene saveene -clusterinfo cluster.info -reservoir reserv/frame -hybridtraj hybrid.strip.crd-ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo -radii radii]
Consult the manual for additional options.
[euphoria.imb.uq.edu.au:26306] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1
mdfil: Error unknown flag: -y
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip rstdip -mdip mddip -ng numgroup -remlog rem.log -remtype rem.type -rem [0|1|2] -rremd [0|1|2|3] -saveene saveene -clusterinfo cluster.info -reservoir reserv/frame -hybridtraj hybrid.strip.crd-ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo -radii radii]
Consult the manual for additional options.
[euphoria.imb.uq.edu.au:26308] MPI_ABORT invoked on rank 2 in communicator MPI_COMM_WORLD with errorcode 1
mpirun noticed that job rank 1 with PID 26307 on node euphoria.imb.uq.edu.au exited on signal 15 (Terminated).
1 additional process aborted (not shown)
mdfil: Error unknown flag: -y
usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
[-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf mdinfo -radii radii]
Consult the manual for additional options.
Error: Sander error! GB mdout file not created.
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
Thanks for your help in advance!
Rilei Yu
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Received on Sat Apr 03 2010 - 03:00:03 PDT
