Dear David,
Thank you very much.
Mijiddorj
On Thu, Mar 31, 2016 at 2:24 AM, David A Case <david.case.rutgers.edu>
wrote:
> 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 Thu Mar 31 2016 - 07:00:04 PDT
