AMBER Archive (2003)

Subject: Re: Sander_classic output: NAN

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 14 2003 - 17:27:17 CDT

On Mon, Jul 14, 2003, pantelo_at_okstate.edu wrote:

> I am running a simple minimization of RB69, Pol-alpha, using sander_classic.
> Below is my input file. I am using .prmtop and .inpcrd files before any
> water or ions have been added. I am having a problem with my output file
> numbers. After the first run, I get "nan" values for everything. Do you
> think it is a problem with my structure or with my input file?

It looks like a problem with the corrdinates, since the 1-4 interactions
are the ones that are blowing up. It is mostly likely that two atoms have
identical coordinates.

>
> Input:
>
> Relaxation of Hydrogen holding all heavy atoms still
> &cntrl
> ntpr=1,
> ntf=1, idiel=0, dielc=1, scnb=2, scee=1.2, cut=10.0
> imin=1, maxcyc=100, ncyc=100, ntmin=1, ntwe=10, ntwxm=0,
> ntr=1, ntwx=1, ntwem=0,
> &end
> Group input for restraining the Protein and DNA heavy atoms
> 5000

I would suggest using a force constant 100 to 1000 times smaller than that
above.

> FIND
> * * M *
> SEARCH
> RES 1 934
> END
> END
>
>
> Output after one step:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 nan nan 3.9408E+08 O 16661
>
> BOND = 903.6790 ANGLE = 2606.6465 DIHED = 8287.9576
> VDWAALS = 23532619.7971 EEL = -24232.1835 HBOND = 0.0000
> 1-4 VDW = nan 1-4 EEL = inf CONSTRAINT = 0.0000
>

..good luck..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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