In addition to what Jason said, yes, that is correct for trehalose.
Of course, we always recommend opening the prmtop and inpcrd in vmd to
make sure the molecule looks right. Just don't forget for Amber 10 to
use scee=1 and scnb=1 in your control file.
:-) Lachele
On Mon, Jan 24, 2011 at 7:17 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 24 2011 - 06:30:02 PST
