On Mon, Jan 24, 2011 at 6:47 PM, subrata paul <paul.subrata34.gmail.com>wrote:
> Dear sir
>
> I make a pdb file for my trehalose concentration. and converted into prmtop
> and inpcrd file using xleap -f leaprc.GLYCAM_06 command.
> After that i tried to minimize in amber 10. but when i tried to minimize
> with following input by sander it takes to many time ,does not showing any
> error, when i put sander comman it remains as it is. why does it happening?
> min.in
> &cntrl
> imin=1,
> maxcyc=150,
> ncyc= 50,
> cut=10,
> /
> How i solve this problem?
> thanking you
> subrata
>
>
>
> On Mon, Jan 24, 2011 at 6:19 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
>
>> 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
>>
>
>
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Received on Mon Jan 24 2011 - 07:00:07 PST
