You could save a PDB of the trehalose molecule and use packmol to create a
solvent box of trehalose and water around your desired solute in the proper
proportions. Knowing the experimental density would probably help. They
key is just to put the proper number of molecules in a given volume of
solution.
Due to the pure massiveness of the mole, lower concentrations will be more
difficult to simulate.
Hope this helps,
Jason
On Mon, Jan 24, 2011 at 12:58 AM, subrata paul <paul.subrata34.gmail.com>wrote:
> Dear sir
>
> I want to simulate 1-6M trehalose solution in amber10.
>
> In xleap -f leaprc.GLYCAM_06
> trehalose=sequence {1GA 0GA}
> Is this ok for makeing trehalose ?
>
>
> How i make 1 - 6 Molar concentration of trehalose solution?
>
>
> thanking you
> subrata
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 24 2011 - 04:30:04 PST
