From chemistry-request: at :server.ccl.net Tue Jun 4 22:35:42 2002 Received: from web21303.mail.yahoo.com ([216.136.129.192]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g552ZgF30766 for ; Tue, 4 Jun 2002 22:35:42 -0400 Message-ID: <20020605023541.52016.qmail "-at-" web21303.mail.yahoo.com> Received: from [203.196.129.98] by web21303.mail.yahoo.com via HTTP; Wed, 05 Jun 2002 03:35:41 BST Date: Wed, 5 Jun 2002 03:35:41 +0100 (BST) From: =?iso-8859-1?q?Ishita=20sharma?= To: chemistry%!at!%ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit 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 __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page > from News and Sport to Email and Music Charts http://uk.my.yahoo.com