AMBER Archive (2008)

Subject: Re: AMBER: NAB to calcuate entropy

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 19 2008 - 19:33:59 CST

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 leap.in -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)
> 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 -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:

   http://structbio.vanderbilt.edu/archives/amber-archive/2008/0448.php

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.]

...dac

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