AMBER Archive (2002)

Subject: Re: Ewald

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 13 2002 - 10:09:08 CST

On Wed, Nov 13, 2002, Monica wrote:

> Dear all, I am using AMBER6 for to minimize my Drug-DNA complex when I run
> minimization in vacuum I got following error:
>
> | peek_ewald_inpcrd: Box info not found in inpcrd
> EWALD SPECIFIC INPUT:
> -------------------------------------------------
> NO EWALD INPUT FOUND: USING DEFAULTS
> -------------------------------------------------
> Largest sphere to fit in unit cell has radius = 0.000
> Ewald PARAMETER RANGE CHECKING:
> parameter skinnb+cutoffnb: (nonbond list cut) has value 0.10000E+02
> This is outside the legal range
> Lower limit: 0.00000E+00 Upper limit: 0.00000E+00
> Check ew_legal.h
>
> What shall I do.Why It has showing Lower limit and Upper limit same i.e.
> 0.00000E+00.

I can't tell whether you have received the reply I sent yesterday (see below).
The problem sounds very similar: check you input value for ntb (default is 1);
if that doesn't help, you will need to provide more information (input files,
etc.). If you indeed tried what I suggested and it didn't work, let us know
that as well (again with relevant details).

..dac

-------------------------------------------------------------------------------
Yesterday's response:
On Tue, Nov 12, 2002, Monica wrote:

> I am running DRU-DNA complex on AMBER6 in vacuum....

> My input file is:
>
> B&cntrl
> imin=1, ncyc=50, maxcyc=1000, nmropt=1, cut=8.0,
> ntpr=100, ntb=1, scee=1.2, ntr=1, scee=1.2
> &end

Setting ntb=1 implies you have a periodic simulation, not a vacuum. My
recollection was that we also recommended using sander_classic for vacuum
calculations in Amber 6. You can get things to work in sander (check the
instructions or the mail archives carefully), but this was less efficient
than running the calculation with sander_classic. 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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