[AMBER] How to visualize modes obtained from NMA

From: The Cromicus Productions <thecromicusproductions.gmail.com>
Date: Wed, 2 Nov 2016 14:23:30 -0400

I'm completely new to Amber and would like to know how can I visualize
normal modes
from PCA.
What I have done so far is:
-I have created a DNA structure using nuc.nab
molecule m;

m = fd_helix( "abdna", "AAAAAGGGGGCC", "dna" );
putpdb( "nuc.pdb", m, "-wwpdb");

-I have obtained the normal modes using nma.nab
molecule m;
float x[4000], fret;

m = getpdb_prm( "nuc.pdb", "leaprc.ff14SB", "", 0 );
mm_options( "cut=999., ntpr=50, nsnb=99999, diel=C, gb=1, 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\fP
mm_options( "ntpr=1" );
newton( x, 3*m.natoms, fret, mme, mme2, 0.00000001, 0.0, 6 );

// get the normal modes:
nmode( x, 3*m.natoms, mme2, 10, 0, 0.0, 0.0, 0);

Now, I get a file called vecs, but what can I do with it to see the modes?

Thanks a lot!
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Received on Wed Nov 02 2016 - 11:30:02 PDT
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