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/ =
-----------------------------------------------------------
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
>>
>
>
>
> --
> 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
>
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Received on Fri Dec 14 2012 - 12:30:04 PST
