Hi,
Are you sure the relavent prmtop file is in the same working directory as
the one you're trying to run MMPBSA in?
Best,
Kenneth
On Monday, October 12, 2015, Ayesha Kanwal <ayesha_comsian.hotmail.com>
wrote:
> yes ras-raf.prmtop file is existing and can also open in text editor and
> i also read introducory tutorial
> how can i make sure that this file is existing why terminal gave this
> error ?
> when i first time run this file i was working but mmpbsa.py didnot work
> then i change the directory newly installed ambertools15 and then rerun
> this file but now at this time it is giving errors how can i solve this
> problem ?
>
> > Date: Mon, 12 Oct 2015 08:34:21 -0600
> > From: daniel.r.roe.gmail.com <javascript:;>
> > To: amber.ambermd.org <javascript:;>
> > Subject: Re: [AMBER] Error: ptraj is needed for MMPBSA
> >
> > Hi,
> >
> > On Mon, Oct 12, 2015 at 7:48 AM, Ayesha Kanwal
> > <ayesha_comsian.hotmail.com <javascript:;>> wrote:
> > > IOError: Could not open ras-raf.prmtop for reading
> >
> > This is the relevant error message. You need to make sure this file
> > exists and that you can access it (i.e. open it with a text editor).
> >
> > You may want to do some introductory tutorials to become a bit more
> > familiar with Amber as a whole
> > (http://ambermd.org/tutorials/#basic_tut).
> >
> > Hope this helps,
> >
> > -Dan
> >
> > > Exiting. All files have been retained.
> > >
> > >
> > >
> > >
> > >
> > >> Date: Sun, 11 Oct 2015 11:28:47 -0400
> > >> From: jason.swails.gmail.com <javascript:;>
> > >> To: amber.ambermd.org <javascript:;>
> > >> Subject: Re: [AMBER] Error: ptraj is needed for MMPBSA
> > >>
> > >> On Sun, Oct 11, 2015 at 10:30 AM, Ayesha Kanwal <
> ayesha_comsian.hotmail.com <javascript:;>>
> > >> 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 <javascript:;>
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org <javascript:;>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> > _______________________________________________
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>
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Received on Mon Oct 12 2015 - 08:30:03 PDT
