AMBER Archive (2008)

Subject: Re: AMBER: NAB to calcuate entropy

From: Z. Nevin Gerek (Nevin.Gerek_at_asu.edu)
Date: Wed Feb 20 2008 - 14:38:28 CST

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.

Nevin

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
>> 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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