Hi,
Again i download ras-raf_top_mdcrd file and put it in AMBERHOME but now it this file is showing different errors as shown below i want to run this file but it did not give me any output file . what is the meaning of the errors? how can i run it correctly ?
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y ras-raf_top_mdcrd.mdcrd
/usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11: ModuleDeprecationWarning: The oldnumeric module will be dropped in Numpy 1.9
warnings.warn(_msg, ModuleDeprecationWarning)
Loading and checking parameter files for compatibility...
File "/home/ayesha/Documents/amber14/bin/MMPBSA.py", line 102, in <module>
app.loadcheck_prmtops()
File "/home/ayesha/Documents/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 572, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File "/home/ayesha/Documents/amber14/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py", line 98, in __init__
self.complex_prmtop = LoadParm(complex_prmtop)
File "/home/ayesha/Documents/amber14/lib/python2.7/site-packages/chemistry/amber/readparm.py", line 63, in LoadParm
parm = AmberFormat(parmname)
File "/home/ayesha/Documents/amber14/lib/python2.7/site-packages/chemistry/amber/amberformat.py", line 365, in __init__
self.rdparm(fname)
File "/home/ayesha/Documents/amber14/lib/python2.7/site-packages/chemistry/amber/amberformat.py", line 436, in rdparm
ret = _rdparm.rdparm(fname)
IOError: Could not open ras-raf.prmtop for reading
Exiting. All files have been retained.
> Date: Sun, 11 Oct 2015 11:28:47 -0400
> From: jason.swails.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Error: ptraj is needed for MMPBSA
>
> On Sun, Oct 11, 2015 at 10:30 AM, Ayesha Kanwal <ayesha_comsian.hotmail.com>
> wrote:
>
> > and when i configure MMPBSA.py it show the following warning
> >
> > ayesha.ayesha-Inspiron-3521[bin] ./MMPBSA.py [
> > 7:27PM]
> > /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11:
> > ModuleDeprecationWarning: The oldnumeric module will be dropped in Numpy 1.9
> > warnings.warn(_msg, ModuleDeprecationWarning)
> > InputError: No input file was provided!
> > Enter `MMPBSA.py --help` for help
> > how can i resolve this problem?
> >
>
> You didn't even try to run MMPBSA.py! You just typed the name of the
> program. It couldn't find any input file, so it complained and quit. The
> deprecation warning is just that -- it's a warning (probably arising from
> the fact that you have ScientificPython installed, but it is not related to
> MMPBSA.py).
>
> I'm not at all sure what you expected to happen, but it behaved the way it
> was supposed to.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Oct 12 2015 - 07:00:04 PDT
