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
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Received on Mon May 30 2011 - 19:00:03 PDT
