AMBER Archive (2003)

Subject: Re: can not minimize

From: Guanglei Cui (cuigl_at_morita.chem.sunysb.edu)
Date: Mon May 05 2003 - 09:07:39 CDT

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