AMBER Archive (2003)

Subject: Re: can not minimize

From: tang kwa (nongtangkwa_at_yahoo.com)
Date: Mon May 05 2003 - 08:57:40 CDT

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
> >
> >
> > __________________________________
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>
> --
> Guanglei Cui
> Dept. of Chemistry
> SUNY at Stony Brook
> Stony Brook, NY 11790
>

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