Dear AMBER users,
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.
*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?
The content of nmode.in is:
"
&data
ntx =1,
ntrun=1, nvect=100,
drms=10,
dielect=1.0, idiel =1,
scnb = 1.0, scee=1.2,
cut =12.0,
t=1.0,
ilevel=0,
ivform=1,
\
"
*2.* My second question is about the NAB method.
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);
"
*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?
Thanks in advance,
Robert
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Received on Mon May 30 2011 - 16:30:02 PDT
