[AMBER] [Amber] Calculating Normal Modes with Restrictions

From: The Cromicus Productions <thecromicusproductions.gmail.com>
Date: Mon, 21 Nov 2016 20:00:26 -0500

Hi everyone,

thanks for your previous replies, you've been very helpful!
I'm currently working with NMA in nab. I can simulate the modes
and get the frequencies with the code below. I'm working with DNA.
Say I want to pin both extremes (residues 1,10,11 and 20 for example)
for my NMA to see "perfect wave" motions, is this possible? What should
I modify to the code?

Thanks a lot,



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, 2000, 0, 0.0, 0.0, 0);
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Received on Mon Nov 21 2016 - 17:30:03 PST
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