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
> To: amber.ambermd.org
> 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> 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
> >> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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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Received on Mon Oct 12 2015 - 08:00:05 PDT
