From chemistry-request@server.ccl.net Sat Sep 1 03:46:27 2001 Received: from janus.hosting4u.net ([209.15.2.37]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f817kRM31542 for ; Sat, 1 Sep 2001 03:46:27 -0400 Received: (qmail 19417 invoked from network); 1 Sep 2001 07:46:27 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 1 Sep 2001 07:46:27 -0000 Received: from yersina ([210.50.62.84]) by proinformatix.com ; Sat, 01 Sep 2001 02:46:24 -0500 Reply-To: From: "Sergio Manzetti" To: "Gromacs Mailring" , "Chemistry Discussion G" Subject: GROMACS Date: Sat, 1 Sep 2001 17:44:51 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Hello everyone. I wish to nominate two chains (A and B from the PDB file) in the *ndx file. HOw should it look like? Chain_A is not recognized. Where can I find a description of the what the nearly 60 energies and variables are, which are calculable in the g_energy script? I am simulating two chains, one enzyme and one inhibitor (A and B), I have read the whole manual, but I just can't figure out how to determine the qualities of interaction between these two under an interval of 100ps. Can someone help me on this please? Thank you Sergio ____________________________________________________________________________ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/