Also, do not put mpirun -np 4 before MMPBSA.py. You do not want to
start 4 threads of this process (since MMPBSA.py itself uses "mpi_cmd"
inside the script, you'll wind up with 16 threads on this node, all of
which will be overwriting each other and in general causing chaos!).
For the rest of the issues, see Bill's email.
On Sat, Apr 3, 2010 at 8:15 AM, Bill Miller III <brmilleriii.gmail.com> wrote:
> There appears to be two different problems here. First, the "unknown flag:
> -y" error means that sander is not recognizing the -y flag that is used for
> post-processing of trajectory files. You should apply the bug fixes for
> amber 10 (http://ambermd.org/bugfixes10.html) and recompile AMBER. There was
> a bug fix (bugfix.4, I believe) that fixes this error. The second error,
> "Error! Ptraj failed. Check coordinate and topology files for the complex."
> is more ambiguous and it is difficult to see what is wrong given the
> information you have provided. However, I noticed that you have specified
> ligand_mask and receptor_mask. You should not have to do this because there
> is a built-in mask guesser that should correctly choose these masks (and you
> can check in the output to see that it was correct). Also, you requested
> analysis on 50 frames, but ptraj only successfully read in 6 frames, which
> means there is some prmtop/mdcrd inconsistency. Since you set
> initial_traj=1, then your trajectory file has no waters or ions, correct?
> Did you give MMPBSA.py a solvated prmtop by chance? This would explain the
> discrepancy in the requested frames versus the output frames.
>
> Good luck!
>
> -Bill
>
> On Sat, Apr 3, 2010 at 6:17 AM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
>
>> 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
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Apr 03 2010 - 07:00:02 PDT
