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
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Received on Thu Sep 30 2010 - 07:00:07 PDT
