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
+ --------------------------------------------------------------------------
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Received on Mon Jul 16 2012 - 20:00:02 PDT
