AMBER: NAB to calcuate entropy

From: Wang, Xuelin <>
Date: Tue, 19 Feb 2008 17:58:15 -0600

Dear amber users

I am using NAB to calculate the entropy of ligand-protein complex. the below is my input:

molecule m;
float x[5749], fret;

m = getpdb_prm( "test1.pdb","leaprc.ff99", "", 0 );
mm_options( "cut=16.0, ntpr=50, gb=1, gbsa=1" );
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);
//printf("congrad returns %d\n",ier);

//Newton-Raphson minimization
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, 0);

but I got the following error message:

Running: /ibis/users_linux/xuelin/nab-5.1.2/bin/teLeap -s -f -I/ibis/users_linux/xuelin/nab-5.1.2/leap/cmd -I/ibis/users_linux/xuelin/nab-5.1.2/leap/parm -I/ibis/users_linux/xuelin/nab-5.1.2/leap/prep -I/ibis/users_linux/xuelin/nab-5.1.2/leap/lib > tleap.out
Reading parm file (tprmtop)

        mm_options: cut=16.0
        mm_options: ntpr=50
        mm_options: gb=1
        mm_options: gbsa=1
    iter Total bad vdW elect. cons. genBorn frms
ff: 0 -8576.17 7735.94 -1750.28 -10638.24 64.21 -3987.79 1.81e+01
        mm_options: ntpr=1
ff: 1 25349557291.95 25349573605.27 -1751.25 -10638.73 64.21 -3987.55 6.32e+04
    iter Total bad vdW elect. cons. genBorn frms
allocation failure in vector: nh = -4615705935918599061
FATAL: allocation failure in vector()

Is my system too large to run?


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Received on Wed Feb 20 2008 - 06:07:39 PST
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