Please see my last email, it contained the instructions you want.
On Wed, Feb 27, 2013 at 10:03 AM, Rasha Alqus
<rasha.alqus.manchester.ac.uk>wrote:
> Dear Amber users,
>
> can you please explain for me the how to do the solution that Janson
> suggested regarding the command arrgument line as janson mentioned below in
> orginal email {Also, the command-line flags that nmode takes will not be
> recognized by
> your nab program -- you already hard-coded the file names into your nab
> program, so you can eliminate all of the command-line arguments.
>
>
>
> ________________________________________
> From: Jason Swails [jason.swails.gmail.com]
> Sent: 26 February 2013 17:01
> To: AMBER Mailing List
> Subject: Re: [AMBER] error in nmode
>
> On Tue, Feb 26, 2013 at 11:46 AM, Rasha Alqus
> <rasha.alqus.manchester.ac.uk>wrote:
>
> >
> >
> >
> > Dear Amber user,
> >
> > Am trying to calculate the raman vibrational frequancy of (C-O) of a
> > macromolecule , using the script below in file G17-vac-nmde.in:
> >
>
> Just to clarify -- what you've written below is not a script, it is a
> compiled program. You must compile it using the nab program (which happens
> to be a compiler).
>
>
> >
> >
> >
> > molecule m;
> > float x[1080], fret;
> >
> > m = getpdb("G17-vac-min.pdb");
> > readparm(m, "G17-vac.top");
> > getxyz("G17-vac-min.rst",360,x);
> >
> > mm_options("cut=999, ntpr=10, nsnb=99999, diel=C, gb=0, dielc=1.0");
> > mme_init(m, NULL, "::Z", x, NULL);
> > setxyz_from_mol(m, NULL, x);
> >
> > //conjugate gradient minimization
> > conjgrad(x,3*m.natoms,fret,mme,0.1,0.001,2000);
> >
> > //newton-raphson minimization
> > newton(x,3*m.natoms,fret,mme,mme2,0.00000001,0.0,6);
> >
> > //get normal modes
> > nmode(x,3*m.natoms,mme2,50,0,0.0,0.0,0);
> >
> >
> After you've made this file, you have to compile it. Pretending you named
> it nmode.nab, the command would look something like this
>
> nab nmode.nab
>
> (or "mpinab nmode.nab")
>
> This will create a file called "a.out", which is your program.
>
> First qusetion:whem i submit this job using nmode function (as in the job
> > script (myscript-vac-nmode.sh ) gave me an error in file
> > myscrip-vac-nmode.sh.e36040 could some one tell me what is wrong and how
> to
> > fix it please.
> >
>
> Your script uses the nmode program to try and calculate the normal modes,
> _not_ the program you just wrote. You need to use the program you just
> wrote (_after_ compiling it, of course). Basically, replace
> "$AMBERHOME/exe/nmode" with "/path/to/your/directory/a.out". I'm not very
> familiar with the sun grid engine (only PBS, really), so I can't help much
> in that regard.
>
> Also, the command-line flags that nmode takes will not be recognized by
> your nab program -- you already hard-coded the file names into your nab
> program, so you can eliminate all of the command-line arguments.
>
> second: the
> >
> >
> >
> > second question mme2,50,0,0.0,0.0,0 what it refer for
> >
>
> It's part of the call signature of the nmode function. Look in the
> AmberTools 12 manual at the NAB section for documentation.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Feb 27 2013 - 07:30:04 PST
