On Sat, Jan 02, 2010, Maryam Hamzehee wrote:
>
> In order to save time, I would like to obtain several snapshots of
> mutated form of structures from the wild-type trajectory by atomic
> coordinate removal and calculate the binding energy so in this way it
> is assumed there is no significant structural change upon mutation.
> I performed the mutation and calculate the binding energy using the
> trajectory of wild type of complex of protein. It was observed that
> the values for calculated GBTOT and PBTOT were too high (for example
> 2526564) I think there is something wrong with this method,
It is safe to assume that something indeed is wrong, but there is too little
information given to ascertain the cause. Ignoring structural changes alone
would not lead to errors 2 million kcal/mol.
...dac
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Received on Sat Jan 02 2010 - 06:30:02 PST
