AMBER Archive (2008)

Subject: AMBER: using NAB to calculate normal modes

From: Z. Nevin Gerek (Nevin.Gerek_at_asu.edu)
Date: Fri Feb 15 2008 - 14:24:50 CST

Hello,
I'm using the newton and nmode functions of NAB to predict normal modes.
(I followed section 6.3 of NAB tutorial.) This is the input file I am
using:

---------------------------nmode.nab-------------
molecule m;
float x[1467], fret;

m = getpdb_prm( "1bfeMin.pdb","leaprc.ff96", "", 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);

//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);
---------------------------------------------------

When I run and look at the results, I can not get any meaningful
results. This is the output file I am getting:

------------------
Running: /usr/local/nab-5.1.2/bin/teLeap -s -f leap.in -I/usr/local/
nab-5.1.2/leap/cmd -I/usr/local/nab-5.1.2/leap/parm -I/usr/local/
nab-5.1.2/leap/prep -I/usr/local/nab-5.1.2/leap/lib > tleap.out
Reading parm file (tprmtop)
title:

         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 -4272.34 627.38 -467.20 -3077.11 26.71 -1382.11
3.45e-01
         mm_options: ntpr=1
ff: 1 23457379094.91 23457384046.76 -466.28 -3113.75 26.73
-1398.55 1.90e+05
     iter Total bad vdW elect. cons.
genBorn frms
ff: 1 693863524921317871583232.00 693863524921317871583232.00
-466.28 -3113.81 0.00 -1398.51 nan
  adding 0.00000 to diagonal of the hessian
rms of search direction: nan
For alpha = 0.00000 energy = nan
For alpha = 1.00000 energy = nan
For alpha = 0.50000 energy = nan
For alpha = 0.75000 energy = nan
For alpha = 0.87500 energy = nan
For alpha = 0.93750 energy = nan
For alpha = 0.96875 energy = nan
For alpha = 0.98438 energy = nan
ff: 2 nan nan nan nan 26.80
nan nan
sff2.c:1223: failed assertion `bk > 0.01'
Abort trap
-------------------------------

Anyone can tell me what I am doing wrong? Thanks in advance.

Nevin

On Feb 6, 2008, at 2:37 PM, David A. Case wrote:

> On Wed, Feb 06, 2008, Wang, Xuelin wrote:
>>
>> How can I incorporate NAB to the MM_PBSA calculation (in NMODE
>> part) or
>> I have to use NAB independently?
>
> To start, you would have to use nab independently. After you learn
> that, you
> could of course modify mm-pbsa to automate the process, if you wished.
>
> ...dac
>
> ----------------------------------------------------------------------
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