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 - 11:30:03 PDT
