On Mon, Jun 18, 2012, Brandon Sim wrote:
>
> I am trying to model GDP using AMBER,
> Total number of electrons: 227; net charge: -2
The total charge of GDP in the deprotonated from you specify appears to be -3,
not -2.
> I am trying to model GDP using AMBER, but I am having trouble using
> antechamber. I am familiar with the GDP/GTP parameters located at
> http://www.pharmacy.manchester.ac.uk/bryce/amber#box, but I am assuming
> (though I may be incorrect) that I still have to run antechamber on my GDP
This is incorrect: the GDP files at the website above should have everything
you need.
....dac
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Received on Mon Jun 18 2012 - 14:30:02 PDT
