AMBER Archive (2008)

Subject: RE: AMBER: NAB to calcuate entropy. .

From: Wang, Xuelin (
Date: Wed Feb 20 2008 - 15:21:15 CST


Why is nsnb=99999? Any explanation?


From: [] On Behalf Of Z. Nevin Gerek
Sent: Wednesday, February 20, 2008 2:38 PM
Subject: Re: AMBER: NAB to calcuate entropy. .

Dr. Case and Andreas,
Thanks for your suggestions. I figured out the problem and wanted to share it.
I tried with small protein and I found that you need to define nsnb in mm_options.
When I wrote
mm_options( "cut=999.0, ntpr=50, gb=1, nsnb=99999" );
It worked without any problem.


On Feb 19, 2008, at 6:33 PM, David A. Case wrote:

On Tue, Feb 19, 2008, Wang, Xuelin wrote:

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

This is incredibly close to a problem reported from just last week:

Please look at that answer. You need to do the same thing: figure out how
to minimize your structure before you can think about normal modes.

allocation failure in vector: nh = -4615705935918599061
FATAL: allocation failure in vector()

How big is your system? Why did you dimension "x" as 5749, which is not
divisible by 3?

[It looks like there may be something that both you and Z.N. Gerek are doing
wrong, which better documentation could remedy. But there is so little
information given in either post that I don't know how to help. Please start
with a *small* system, do its normal modes, and then work your way up.]


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