Thank you the answers prof. Case!
There is attached the nmode.out.
You write that I have to use a much bigger cut off radius, for a better
minimizaion. For MD simulation, let say simulated annealing, is cut=12 good?
Can you give me some turotial about how to analyse the modes? I've got
somewhere an example with ptraj, but I dont understand well.
Best wishes,
Robert
2011/5/31 case <case.biomaps.rutgers.edu>
> On Tue, May 31, 2011, Deák Robi wrote:
> >
> > I want to make NMA of a protein and I tried the nmode and NAB method too.
> I
> > minimized the structure with sander and relaxed it on 0K over 2ns with
> > sander.
>
> This generally won't be nearly stringent enough a minimum to do normal mode
> analysis.
>
> >
> > *1.* My first question is about nmode.
> > The nmode (nmode -O -i nmode.in <http://nmode1.in/> -o nmode.out -p
> 0.prmtop
> > -c 0.inpcrd -v vecs) didn't produce anything in the vecs file, can
> somebody
> > explain me why?
>
> What is in the nmode.out file? My best guess (see above) is that you don't
> have a fully minimized structure. Note that you need to use an infinite
> cutoff (or some very specialized techniques) to generate a fully-minimized
> structure. But the nmode.out file tells you what has been happening.
>
> > With this method the vecs file is not empty, but in the output I realize
> > some negative frequencies(with and without NAB minimization (conjgrad +
> > newton) too). Does these means imaginary frequencies? If yes, what can I
> do
> > to eliminate them?
> > The content of the nab script is:
> > "
> > molecule m;
> > float x[12000], fret;
> > m = getpdb_prm( "0.pdb", "leaprc.ff99SB", "", 0);
> > mm_options( "cut=12.0, ntpr=10, nsnb=9999, diel=C, gb=0, dielc=1.0,
> > temp0=0.0" );
> > mme_init( m, NULL, "::Z", x, NULL);
> > setxyz_from_mol( m, NULL, x );
> > nmode( x, 3*m.natoms, mme2, 50, 0, 0.0, 0.0, 0);
>
> Again, you need to force minimization to a very low level, and set cut to
> 9999. or something much bigger than the size of your system. Be sure the
> that
> rms of the gradient vector elements is less than 10**-7 or so. If you call
> nmode() from a non-minimized structure, it won't complain (because this
> capability is needed for so-called 'instanteous mode' analysis), but you
> will
> see negative (==imaginary) frequencies.
>
> Take a look at the asp.nab script in $AMBERHOME/AmberTools/test/nab to get
> some sample code. This forces the rms gradient to be 10**-12, which is
> doable
> but perhaps overkill.
>
> > *3.* The third question is about vecs.
> > This is the output of the modes in amber format. Can somebody tell me
> about
> > this format(or send a description)? How can be extracted the eigenvalues
> and
> > the vectors?
>
> Best doc here right now is the code that reads/writes these files.
> Basically,
> the coordinates are in the first block, then each eigenvalue (expressed, I
> think as a frequency in cm**-1) followed by the eigenvector. It's all
> plain
> text, so you can study it with a text editor.
>
> ....dac
>
>
> _______________________________________________
> 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
Received on Tue May 31 2011 - 01:00:02 PDT
