From owner-chemistry@ccl.net Thu Jul 18 02:56:00 2013 From: "Jacco van de Streek jacco.vandestreek*o*sund.ku.dk" To: CCL Subject: CCL: Generating neighboring molecule Message-Id: <-48971-130718025323-9677-/sJF2B0kYRkqBwnBe+4mmQ(!)server.ccl.net> X-Original-From: Jacco van de Streek Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 18 Jul 2013 06:52:50 +0000 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [jacco.vandestreek{}sund.ku.dk] > I have a .cif of a molecule from the literature. I want to do a calculation on > its dimer. The authors give the transformation to generate the neighboring > molecule (the .cif does not include the dimer). What software could I use to > help me generate the molecule? I have chemcraft and jmol but any other program > suggested works would be fine as well. The program that Brad Rose suggests is indeed one of the best programs for visualising and analysing crystallographic files. The program is called Mercury: http://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx It is free and it is available for multiple operating systems. It is distributed by the Cambridge Crystallographic Data Centre (CCDC). Read the cif into Mercury and either: 1. switch on "Packing" and delete the excess molecules or 2. switch on "H-bond" and click on the hydrogen bond you are interested in to expand the contact into a full molecule and generate the dimer (if the dimer is hydrogen-bonded). If the dimer is not hydrogen bonded, you may try the same trick with "Short Contact". Mercury can export the atoms that you see on the screen to a .xyz file. Best wishes, -- Dr Jacco van de Streek Department of Pharmacy University of Copenhagen From owner-chemistry@ccl.net Thu Jul 18 12:19:01 2013 From: "David Soriano del Amo d.soriano:acellera.com" To: CCL Subject: CCL: webinar on high-throughput molecular dynamics July 25 9am PST Message-Id: <-48972-130718083904-25531-0v9w3FncpZbswS+Htd4IlA-x-server.ccl.net> X-Original-From: "David Soriano del Amo" Date: Thu, 18 Jul 2013 08:39:02 -0400 Sent to CCL by: "David Soriano del Amo" [d.soriano^acellera.com] Hi all, I would like to announce the webinar in high-throughput molecular dynamics simulations July 25th 9am PDT. See the following link for more information. https://www2.gotomeeting.com/register/682734778 Do not miss this great opportunity to learn about the latest on how to best exploit GPUs for your MD needs, especially for probing ligand-receptor interactions. Cheers!