Hi,
In addition to Hai's suggestion, you could also find an existing beta
sheet structure you could use as a template in conjunction with the
'loadpdbusingseq' command in tleap, which will replace the input PDB
sequence with a specified one. Be aware however that leap doesn't
automatically resolve clashes that result from this, so you may have
to put in some extra work to resolve those. Hope this helps,
-Dan
On Wed, Oct 28, 2015 at 11:22 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> I have not tried the complicated system but seem to me cpptraj can do it
> with '*makestructure*' command. check amber15 manual, page 549.
>
> What I have in mind is to use tleap to generate linear structure, then
> using cpptraj to tweak it.
>
> Alternative you can google or try *modeller *program
>
> Hope this help
>
> Hai
>
> On Wed, Oct 28, 2015 at 1:13 PM, Jagannath Mondal <jmondal.backup.gmail.com>
> wrote:
>
>> Dear all
>>
>> Is there a tool or method to generate coordinates of a model beta sheet
>> structure for a given sequence ?
>>
>> Jagannath
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Oct 29 2015 - 08:00:04 PDT
