Hi,
crankite is a easy to use software to build random peptides or you could
use ECEPP package developed on Scheragas team.
H.A.B.
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
>
--
---------------------------------------
Dr. Hector A. Baldoni
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917
5700 San Luis - Argentina
hbaldoni.unsl.edu.ar
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Received on Fri Dec 14 2012 - 16:00:02 PST
