Dear David,
If I want to make hydrophilic solutions, practically, what kind of
molecules suitable?
Thank you again.
Mijiddorj
On Thu, Mar 31, 2016 at 10:53 PM, Mijiddorj Batsaikhan <
b.mijiddorj.gmail.com> wrote:
> 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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>>
>
>
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Received on Sat Apr 02 2016 - 02:00:03 PDT
