Thank you very much, Ilyas, for this suggestion. My peptides are not too
large (6 to 8 amino acids). simulated annealing with no constraints may
yield good random starting points for my subsequent simulations.
thanks again,
shashi
On Fri, Dec 14, 2012 at 3:10 PM, Ilyas Yildirim <i-yildirim.northwestern.edu
> wrote:
> Just a suggestion - simulated annealing can be a good procedure to create
> random conformations. I assume you want random conformations for folded
> state for a protein. Extend the two ends (using distance restraints) and do
> simulated annealing. Do this procedure as many times as you want; extend
> and let the system fold to a state. At the end, you can cluster the
> structures and use the unique ones.
>
> Best,
>
> Ilyas Yildirim, Ph.D.
> ------------------------------**-----------------------------
> = Department of Chemistry - 2145 Sheridan Road =
> = Northwestern University - Evanston, IL 60208 =
> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> = http://www.pas.rochester.edu/~**yildirim/<http://www.pas.rochester.edu/~yildirim/> =
> ------------------------------**-----------------------------
>
>
>
> On Fri, 14 Dec 2012, Shashidhar Rao wrote:
>
> Hi Jason,
>>
>> thanks for the clarification. I will do a detailed Google search to see
>> what is available for building random conformations of peptides. I came
>> across something called "CRANKITE" in the quick survey.
>>
>> shashi
>>
>> On Fri, Dec 14, 2012 at 2:58 PM, Jason Swails <jason.swails.gmail.com
>> >wrote:
>>
>> On Fri, Dec 14, 2012 at 2:20 PM, Shashidhar Rao <shashidharr.gmail.com
>>>
>>>> wrote:
>>>>
>>>
>>> I would like to know if it is possible to build a random conformation of
>>>>
>>> a
>>>
>>>> peptide in AMBER (tleap) instead of the extended linear chain which can
>>>>
>>> be
>>>
>>>> minimized and subjected to dynamics to generate arbitrary conformations.
>>>>
>>>>
>>> No. tleap will only build from templates (resulting in, as you've seen,
>>> linear chains when no existing coordinates exist). You will have to
>>> build
>>> the structure in a random conformation some other way, then load the
>>> resulting PDB into tleap.
>>>
>>> Good luck,
>>> Jason
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> ______________________________**_________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/**mailman/listinfo/amber<http://lists.ambermd.org/mailman/listinfo/amber>
>>>
>>>
>>
>>
>> --
>> Shashidhar N. Rao
>> 3 SERINA DRIVE
>> PLAINSBORO
>> NEW JERSEY 08536 USA
>>
>> shashidharr.gmail.com
>> ______________________________**_________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/**mailman/listinfo/amber<http://lists.ambermd.org/mailman/listinfo/amber>
>>
>>
--
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr.gmail.com
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Received on Fri Dec 14 2012 - 13:30:02 PST
