[AMBER] Freeze Atoms in Nab

From: The Cromicus Productions <thecromicusproductions.gmail.com>
Date: Fri, 9 Dec 2016 16:05:12 -0500

Hi everyone,

I'm trying to perform NMA with some atoms frozen but I seem to keep
walking into errors. Let's say I want to freeze the atoms 1-30,287-349,
606-638. I tried to use the following nma.nab code:

molecule m;
float x[4000], x0[4000],fret;
file file1;
file1=fopen("outx", "w" );

m = getpdb_prm( "nuc.pdb", "leaprc.ff14SB", "", 0 );
mm_options( "cut=999., ntpr=50, nsnb=99999, diel=C, gb=1,
dielc=1.0,wcons=20.0" );
setxyz_from_mol( m, NULL, x0 );
mme_init( m, NULL, "1:30,287:349,606:638", x0, file1);
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);


But I notice that in the vector file the residues I want to freeze still
move a lot. Any idea of what am I doing wrong? Just in case, I'm attaching
my pdb file.



AMBER mailing list

Received on Fri Dec 09 2016 - 13:30:03 PST
Custom Search