[no subject]



Sir,
        I am pooja,just joined into the field of
 molecular modeling in INDIA.i have a peptide which has
 a sequence
 	 GEWTWDDATKTWTWTEGGGGFALFALFA
 The first part of this sequence that is
 	GEWTWDDATKTWTWTE is known to have a beta-hairpin
 structure and the other part GGGG is a linker FALFALFA
 forms a helix,i wish to know how the peptide will fold
 if i join all these together ,i ahve the pdb file for
 GEWTWDDATKTWTWTE and for the other part i have
 generated using INSIGHTII ,so i have a pdb file for
 the entire sequence which corresponds to a
 beta-beta-alpha motif,i just want to know whether it
 will actually make  this motif using AMBER(molecular
 dynamics and minimisation).Is AMBER the correct choice
 or should i use some other software as i have been
 told that it is not necessary that AMBER would predict
 the correct structure,do you have any idea where else
 this kind of peptide structure prediction studies are
 carried out.
                   Waiting for your reply
                       Thanks
                              with regards
                               pooja
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