Am Donnerstag, den 30.09.2010, 09:35 -0400 schrieb case:
> On Thu, Sep 30, 2010, Kirsten Heitmann wrote:
> >
> > I have a problem with the Thermodynamic Integration:
> > I want to mutate an adenine into a thymine (the first and last base from
> > an 10 base-pair long DNA). And during the
> > last step, when adding the charges to the thymine at the lambda steps
> > 0.1, 0.3 and 0.4 the calculation stops without an error message. The
> > curios thing is, that the programs runs without any
> > problems at other lambda steps 0.2, 0.5, 0.6, 0.7, 0.8 and 0.9.
>
> > icfe = 1, clambda = > 0.1,
> > ifsc=0,
> > crgmask=':1,10,11,20',
>
> This doesn't look right: in changing A to T you are making atoms disappear; to
> do that you should use the softcore option. This is a very advanced option,
> so start small, say with just the base (or nucleotide) by itself (in water, no
> other nucleotides). You should first remove the charges on the atoms that
> will disappear, then use softcore to decouple those atoms from the solvent,
> then add back in charges appropriate to thymine.
>
> ...good luck....dac
What do you describe is what I have done. In a first step I have removed
the charges on the specified atoms than use softcore. This was done
without any problems and then I want to add the charges to the specific
atoms, and then the problem occurs.
Kirsten Heitmann
>
>
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Received on Thu Sep 30 2010 - 10:00:09 PDT
