The errors suggests that "M11-L112A.gas.prmtop" is a command, which means
the MMPBSA.py command line was not written properly in your jobfile.
Without seeing the command line you attempted, it is difficult to diagnose
the exact problem. But make sure there is an option (-sp, -cp, -rp, etc)
before each file name.
I hope that helps.
-Bill
On Mon, Jul 16, 2012 at 10:55 PM, Delwar Hossain <hossaind2004.yahoo.com>wrote:
> Hi,
> I am trying to use MMPBSA.py script in amber 11. When I run the script I
> get error message:
> i) Error: Command line error!
> ii) M11-L112A.gas.prmtop: Command not found.
>
> I therfore request you to help me to solve this problem.
> Thank you.
> Delwar
>
>
> Input file:
> Input file for running PB and GB
> &general
> endframe=50, verbose=1,
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.000
> /
> &pb
> istrng=0.000,
> /
> Output:
> Warning: no access to tty (Bad file descriptor).
> Thus no job control in this shell.
> ModuleCmd_Switch.c(172):ERROR:152: Module 'PrgEnv-cray' is currently not
> loaded
> ModuleCmd_Switch.c(172):ERROR:152: Module 'PrgEnv-cray' is currently not
> loaded
> Reading command-line arguments and input files...
> Error: Command line error!
> Usage: MMPBSA.py {-O} -i inputfile \
> -o output_file \
> -sp solvated_prmtop \
> -cp complex_prmtop \
> -rp receptor_prmtop \
> -lp ligand_prmtop \
> -y mdcrd1 mdcrd2 mdcrd3 ... mdcrdN \
> {-do decomp_output_file} \
> {-yr receptor_mdcrd1 ... receptor_mdcrdN} \
> {-yl ligand_mdcrd1 ... ligand_mdcrdN} \
> {-mc mutant_complex_prmtop} \
> {-mr mutant_receptor_prmtop} \
> {-ml mutant_ligand_prmtop} \
> {-srp solvated_receptor_prmtop} \
> {-slp solvated_ligand_prmtop} \
> {-xvvfile xvvfile} \
> {-make-mdins} || {-use-mdins} || {-rewrite-output}
> M11-L112A.gas.prmtop: Command not found.
> +
> --------------------------------------------------------------------------
> + Job name: test_amber
> + Job Id: 1933776.sdb
> + System: hopper
> + Queued Time: Mon Jul 16 18:05:00 2012
> + Start Time: Mon Jul 16 18:54:57 2012
> + Completion Time: Mon Jul 16 18:55:02 2012
> + User: dhossain
> + MOM Host: nid04132
> + Queue: reg_1hour
> + Req. Resources: other=QSUBPID:28935:hopper12,walltime=00:30:00
> + Used Resources: cput=00:00:00,mem=0kb,vmem=0kb,walltime=00:00:05
> + Acct String: m1368
> + PBS_O_WORKDIR: /global/homes/d/dhossain/L112A-GBimp
> + Submit Args: mmpbsa4
> +
> --------------------------------------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 17 2012 - 04:00:02 PDT
