hello,
i am trying to derive the charges for a modified amino acid and am working
through the collage of information out there. i am trying to utilize the RED
programs that the RED guys were nice enough to put together. i am using
gaussian for the geo-optimization and charge calculation and the feeding it
into the proper places in the AmberTools suite.
i've convinced myself, using a simple test system, that it is time to move
on to the more complicated, modified amino. i am now kind of confused at the
proper way to go about generating the multiple confirmations necessary to
fit this more complicate molecule. is there a typical way to generate
multiple conformations and orientations for molecules, such as drug
molecules or drug molecules covalently bound to an amino, that have not been
parametrized yet? or if there is no typical way, how do any of you do it?
thank you very much for any help with this topic.
-jz
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Received on Wed Oct 26 2011 - 10:30:02 PDT
