On Thu, Mar 31, 2016, Mijiddorj Batsaikhan wrote:
>
> I would like to simulate a structure of peptide in hydrophobic solution?
> Please give me advice and suggestions? Thank you.
You need to choose a solvent (hexane? ocatanol? benzene?) that matches some
experiment, or that you think is "hydrophobic". Note that Amber assumes
by default that the N- and C-terminal residues are charged, which may not be
the case in non-aqueous solvents. So unless the end residues are not
important to you, you will have to learn how to build neutral residues for
your termini. You should expect a significant learning curve: Amber was
primarily designed for aqeuous simulations, and setting up other types of
environemnts requires a good understanding of how the program works.
....dac
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Received on Wed Mar 30 2016 - 10:30:04 PDT
