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
I am really appreciated for your help!
Rilei Yu
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Received on Sat Apr 03 2010 - 03:30:04 PDT
