From owner-chemistry@ccl.net Thu Sep 11 02:06:00 2008 From: "Vivek Sharma vivek.viv.sharma::gmail.com" To: CCL Subject: CCL: comparison between 2 different structures Message-Id: <-37739-080911020121-20079-lNRRgAoSyrTgHw28gOE41w- -server.ccl.net> X-Original-From: "Vivek Sharma" Date: Thu, 11 Sep 2008 02:01:16 -0400 Sent to CCL by: "Vivek Sharma" [vivek.viv.sharma ~ gmail.com] Dear CCL people, I have one conceptual question to ask, may be its trivial but all your comments will be very helpful in understanding more about this field and will obviosuly correct some doubts. Lets say I have two different ligand molecules (different substituents on some common core). I sketch them, do conformational analysis on those and minimise the energy of both the systems separately and finally some values of total potential energy are obtained. And, if one value is lower than the other, can I say that this molecule (with lower potential energy) is more stable than the other one? I have mixed thoughts about it. I would assume if there have been a single compound, one can compare the potential energies of the compound in two different tautomeric states for example. But in case of two different compounds, which will have different potential energy landscapes, etc, it may not be possible. My this query also scales-up to a docking study where a similar question arises, i.e. can I compare the Binding Energy or Interaction Energy between two different Protein Ligand complexes (where protein is same in both, but ligands are chemically different).? thanks in advance, Vivek IMM, Pune, India. From owner-chemistry@ccl.net Thu Sep 11 13:17:01 2008 From: "Anuradha Mittal anuradha.mittal * gmail.com" To: CCL Subject: CCL: clashes in structure Message-Id: <-37740-080911122050-24819-oRkMn8b9blMgjp6ct8/IJQ**server.ccl.net> X-Original-From: "Anuradha Mittal" Content-Type: multipart/alternative; boundary="----=_Part_119937_7814511.1221145842260" Date: Thu, 11 Sep 2008 10:10:42 -0500 MIME-Version: 1.0 Sent to CCL by: "Anuradha Mittal" [anuradha.mittal:+:gmail.com] ------=_Part_119937_7814511.1221145842260 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all! What all programs can I use for finding clashes in a molecule. I have a structure which is showing a positive free energy. I want to check if it is due to any intramolecular clashes. Any comments will be much appreciated. Thanks in advance Anu ------=_Part_119937_7814511.1221145842260 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi all!

What all programs can I use for finding clashes in a molecule. I have a structure which is showing a positive free energy. I want to check if it is due to any intramolecular clashes.
Any comments will be much appreciated.

Thanks in advance
Anu
------=_Part_119937_7814511.1221145842260-- From owner-chemistry@ccl.net Thu Sep 11 13:53:01 2008 From: "Anuradha Mittal amitta2#%#uic.edu" To: CCL Subject: CCL: clashes in structure Message-Id: <-37741-080911125823-31669-fgmcqWsJBX3C35vqwQRwUA^^server.ccl.net> X-Original-From: "Anuradha Mittal" Content-Type: multipart/alternative; boundary="----=_Part_121572_12181587.1221150669478" Date: Thu, 11 Sep 2008 11:31:09 -0500 MIME-Version: 1.0 Sent to CCL by: "Anuradha Mittal" [amitta2]-[uic.edu] ------=_Part_121572_12181587.1221150669478 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi all! What all programs can I use for finding clashes in a molecule. I have a structure which is showing a positive free energy. I want to check if it is due to any intramolecular clashes. Any comments will be much appreciated. Thanks in advance Anu ------=_Part_121572_12181587.1221150669478 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi all!

What all programs can I use for finding clashes in a molecule. I have a structure which is showing a positive free energy. I want to check if it is due to any intramolecular clashes.
Any comments will be much appreciated.

Thanks in advance
Anu




------=_Part_121572_12181587.1221150669478-- From owner-chemistry@ccl.net Thu Sep 11 14:27:00 2008 From: "Alexandr Isayev alex=ccmsi.us" To: CCL Subject: CCL: extended deadline: 17th Conference on Current Trends in Computational Chemistry Message-Id: <-37742-080911124940-30224-F/VE7DwBkAJoQ93iOifhDQ^server.ccl.net> X-Original-From: Alexandr Isayev Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1250 Date: Thu, 11 Sep 2008 11:49:23 -0500 MIME-Version: 1.0 Sent to CCL by: Alexandr Isayev [alex_-_ccmsi.us] Dear Collegues, We would like to inform you that the registration and abstract submission deadline for the 17th Conference on Current Trends in Computational Chemistry (CCTCC) has been extended through October 1, 2008. This symposium, organized by Jackson State University, covers all areas of computational chemistry as well as quantum chemistry. This year the 17th CCTCC will be held at the Hilton Jackson Hotel, Jackson, Mississippi on October 31 - November 1, 2008. Conference website: http://cctcc.ccmsi.us Flyer: http://cctcc.ccmsi.us/flyer-cctcc08.png (1.8mb) List of invited speakers: Maria Barysz, Nicolaus Copernicus University, Poland Tim Clark, Friedrich=96Alexander University of Erlangen=96Nuremberg=20 Ernest R. Davidson, University of Washington Magdolna Hargittai, Budapest University of Technology and Economics So Hirata, University of Florida Walter Kohn, University of California, Santa Barbara William A. Lester, University of California, Berkeley Vincent Meunier, Oak Ridge National Lab Michel Mons, Commissariat a l=92Energie Atomique, France Ruth Pachter, US Air Force Research Laboratory, Wright-Patterson Air Force = Base Edward J. Perkins, US Army Engineering Research and Development Center Oleg Prezhdo, University of Washington G. Narahari Sastry, Indian Institute of Chemical Technology, India Jorge Seminario, Texas A & M University Priya Vashishta, University of Southern California We are planning to publish extended abstracts (up to four pages each) of all invited talks and poster presentations. For more information and registrati= on, visit our conference Web site at http://cctcc.ccmsi.us with best regards - CCTCC 2008 team On behalf of the Organizing Committee ------------------------------------------------------- Olexandr Isayev, Research Assistant, and System Administrator ++ Computational Center for Molecular Structure and Interactions (CCMSI), Jackson State University, Jackson, MS USA Tel: +(601) 979-1134 e-mail: alex(at)ccmsi.us Web: http://www.ccmsi.us/alex -------------------------------------------------------- From owner-chemistry@ccl.net Thu Sep 11 15:02:00 2008 From: "Elaine C Meng meng__cgl.ucsf.edu" To: CCL Subject: CCL: clashes in structure Message-Id: <-37743-080911135356-24866-ht0dyurEnJR2VyPJHQunJw=-=server.ccl.net> X-Original-From: "Elaine C Meng" Date: Thu, 11 Sep 2008 13:53:52 -0400 Sent to CCL by: "Elaine C Meng" [meng^^cgl.ucsf.edu] Hi Anu, You could use the "Find Clashes/Contacts" feature in Chimera: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html Chimera is free for noncommercial use and can be downloaded for Mac, Windows, Linux from http://www.cgl.ucsf.edu/chimera/download.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng]^[cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html