OK, I will check it. Thank you for your time.
Yours sincerely,
Guoxiong Su
On Mon, Jul 26, 2010 at 1:01 PM, case <case.biomaps.rutgers.edu> wrote:
> On Mon, Jul 26, 2010, Guoxiong Su wrote:
> >
> > I am a new amber10 user. I am trying to use antechamber of Ambertools 1.4
> to
> > get the parameter file for my bioorganic molecule. However, I got these
> > message as below in sqm.out:
> >
> > xmin 170 1246.6672 kcal/mol 0.0035 kcal/(mol*A)
> > xmin 180 1246.6672 kcal/mol 0.0035 kcal/(mol*A)
> > xmin 190 1246.6672 kcal/mol 0.0035 kcal/(mol*A)
> > xmin 200 1246.6672 kcal/mol 0.0035 kcal/(mol*A)
> > xmin 210 1246.6672 kcal/mol 0.0035 kcal/(mol*A)
> > xmin 220 1246.6672 kcal/mol 0.0035 kcal/(mol*A)
> > xmin 230 1246.6672 kcal/mol 0.0035 kcal/(mol*A)
> >
> > And it takes much time to run sqm. So my question is:
> > 1. Is the sqm parallel? If it is, how to do it?
> > 2. Can I change the tolerance? So, it can be converged when I got number
> > like above.
> > 3. Since my molecule is large, can I have other options to do it?
>
> Have you read note 6 on p. 84 of the AmberTools Users' Manual? For "large"
> molecules (how large????) you may need to play with things.
>
> The fact that your energy is positive, rather than negative, however,
> suggests
> that something may be seriously wrong with your structure. Are you sure
> you are starting with a reasonable geometry, that all hydrogen atoms are
> present, etc?
>
>
> ....dac
>
>
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Received on Mon Jul 26 2010 - 11:30:04 PDT
