AMBER Archive (2003)

Subject: Re: can not minimize

From: tang kwa (nongtangkwa_at_yahoo.com)
Date: Mon May 05 2003 - 09:45:24 CDT

Hi,

I changed an input to igb = 0 :
&cntrl
  imin = 1, maxcyc = 500, ntpr = 25,
   igb = 0, ntb = 0, cut = 10.0,
&end

The output shows that

  1. RESOURCE USE:

   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 0.13000E+02
 This is outside the legal range
 Lower limit: 0.00000E+00 Upper limit: 0.88528-250
 Check ew_legal.h

What is the problem? Could you please suggest me? The
PME method will be 'off', if ntb = 0,right?

Thanks,
TK

--- Guanglei Cui <cuigl_at_morita.chem.sunysb.edu> wrote:
> Hi,
> I think hydrogen atom order only affects igb=1.
> If you can rearrange your
> hydrogen atoms, it might solve this ...
>
> On Monday 05 May 2003 09:57, tang kwa wrote:
> > DEAR Guanglei Cui,
> > When I used igb = 2 or 3, it can be run. Is it
> > possible to minimize without IGB? Because I would
> like
> > to minimize in the Vaccum.
> > Thanks,
> > TK
> >
> > --- Guanglei Cui <cuigl_at_morita.chem.sunysb.edu>
> wrote:
> > > Hi,
> > > If I remember correctly, this might be caused
> by
> > > your atom arrangement in
> > > your structure file. You didn't specify which
> > > version of sander you used, but
> > > in sander6, GB used to require that hydrogen
> atoms
> > > follow their bonding heavy
> > > atoms. Otherwise, it will complain and stop.
> (atom
> > > 19 should be a hydrogen
> > > atom if this's the reason). I hope this helps.
> > >
> > > On Monday 05 May 2003 07:57, tang kwa wrote:
> > > > Dear all,
> > > >
> > > > I have a question about the minimization. I
> would
> > >
> > > like
> > >
> > > > to check the frcmod file. So I will compare
> the
> > > > minimized structure from AMBER with Gaussian.
> > >
> > > However
> > >
> > > > I could not minimize the molecule. This is my
> > >
> > > input
> > >
> > > > file:
> > > >
> > > > &cntrl
> > > > imin = 1, maxcyc = 500, ntpr = 25,
> > > > igb = 1, ntb = 0, cut = 10.0,
> > > > &end
> > > >
> > > > the out showed that
> > > > NATOM = 64 NRES = 1
> > > >
> > > > MAXCYC= 500 NCYC = 10 NTMIN = 1
> > >
> > > DX0
> > >
> > > > = 0.010000
> > > > DXM = 0.50000 DRMS = 0.00010
> > > >
> > > > Water definition for fast triangulated
> model:
> > > > Resname = WAT ; Oxygen_name = O ;
> Hyd1_name
> > >
> > > =
> > >
> > > > H1 ; Hyd2_name = H2
> > > > Using modified Bondi radii and Tinker
> screening
> > > > parameters
> > > > Unable to find bonded partner for atom 19
> > > >
> > > >
> > > > I will appreciate it if anybody can figure out
> > >
> > > this
> > >
> > > > problem.
> > > > One more question, is it possible to minimize
> > >
> > > without
> > >
> > > > IGB(IGB=0)?
> > > >
> > > > Thank you in advance,
> > > > TK
> > > >
> > > >
> > > > __________________________________
> > > > Do you Yahoo!?
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> > >
> > > --
> > > Guanglei Cui
> > > Dept. of Chemistry
> > > SUNY at Stony Brook
> > > Stony Brook, NY 11790
> >
> > __________________________________
> > Do you Yahoo!?
> > The New Yahoo! Search - Faster. Easier. Bingo.
> > http://search.yahoo.com
>
> --
> Guanglei Cui
> Dept. of Chemistry
> SUNY at Stony Brook
> Stony Brook, NY 11790
>

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