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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Received on Wed Feb 27 2013 - 07:30:03 PST
