From owner-chemistry@ccl.net Tue Apr 10 00:04:00 2007 From: "Christos Deligkaris cdeligka[A]purdue.edu" To: CCL Subject: CCL: Calculation of Gasteiger charges for charged molecules Message-Id: <-34012-070410000026-14347-PfkhTbAtwIz5NqbE9j6DVw++server.ccl.net> X-Original-From: "Christos Deligkaris" Date: Tue, 10 Apr 2007 00:00:23 -0400 Sent to CCL by: "Christos Deligkaris" [cdeligka() purdue.edu] Dear all, I am looking for a program that can calculate partial charges with the Gasteiger method (partial equalization of orbital electronegativity) for molecules which are not neutral. I have already found programs that can calculate the Gasteiger charges for neutral molecules but I would like to calculate the Gasteiger partial charges for a small molecule that has a formal charge of -1. If anyone is aware of a program free for academic or personal use that can do this calculation, please let me know, Christos Deligkaris From owner-chemistry@ccl.net Tue Apr 10 06:10:01 2007 From: "Alfred Gil Arranz agil:cesca.es" To: CCL Subject: CCL: Scienomics Seminar at CESCA, 20th April Message-Id: <-34013-070410055733-13582-yWOzGPw9yPL7qoCuEGDOdg a server.ccl.net> X-Original-From: Alfred Gil Arranz Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 10 Apr 2007 11:14:59 +0200 MIME-Version: 1.0 Sent to CCL by: Alfred Gil Arranz [agil,+,cesca.es] Dear CCL users, Scienomics and CESCA are pleased to announce a free molecular seminar on the 20th of April based on Scienomics' MAPS version 2.1. MAPS is a complete molecular modeling toolkit, covering classical simulations, quantum mechanics and mesoscale simulations. You can get the Agenda and additional information for the event at: http://www.cesca.es/promocio/congressos/scienomics/Scienomics-CESCA-Seminar-Agenda.pdf We look forward to welcoming you to the Scienomics' MAPS Seminar! -- ...................................................................... __ / / Alfred Gil i Arranz C E / S / C A Departament de Sistemes /_/ Centre de Supercomputació de Catalunya Gran Capitą, 2-4 (Edifici Nexus) · 08034 Barcelona T. 93 205 6464 · F. 93 205 6979 · agil,cesca.es ...................................................................... From owner-chemistry@ccl.net Tue Apr 10 07:40:02 2007 From: "Chris Howard c.k.howard!^!reading.ac.uk" To: CCL Subject: CCL: BiBTeX & LyX Message-Id: <-34014-070410073742-16719-ZBNo5/PuRXyy5Hfd3L33lw++server.ccl.net> X-Original-From: "Chris Howard" Content-Type: multipart/alternative; boundary="----=_NextPart_000_000A_01C77B6D.00641840" Date: Tue, 10 Apr 2007 12:37:28 +0100 MIME-Version: 1.0 Sent to CCL by: "Chris Howard" [c.k.howard.:.reading.ac.uk] This is a multi-part message in MIME format. ------=_NextPart_000_000A_01C77B6D.00641840 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Hi, I am trying to write my Thesis in Lyx however I am finding it really hard to keep my references organised. I was told BiBTeX can be used to control this including the essential tool of sorting my references into order! So basically, does anyone know how to go from a normal lyx version to a bibtex version? All the documentation on the web has utterly confused me. I was hoping for a step by step guide, if anyone has one. All the best, and thank you, Chris ------=_NextPart_000_000A_01C77B6D.00641840 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Hi,

 

I am trying to write my Thesis in Lyx however I am = finding it really hard to keep my references organised. I was told BiBTeX can be = used to control this including the essential tool of sorting my references = into order! So basically, does anyone know how to go from a normal lyx = version to a bibtex version? All the documentation on the web has utterly confused = me. I was hoping for a step by step guide, if anyone has = one.

 

All the best, and thank = you,

 

Chris

------=_NextPart_000_000A_01C77B6D.00641840-- From owner-chemistry@ccl.net Tue Apr 10 08:41:01 2007 From: "Jozsi Szegezdi jszegezdi!=!chemaxon.com" To: CCL Subject: CCL: Calculation of Gasteiger charges for charged molecules Message-Id: <-34015-070410030240-26845-DZuXyjDIq5ZRCSkF9O66hA]|[server.ccl.net> X-Original-From: "Jozsi Szegezdi" Date: Tue, 10 Apr 2007 03:02:36 -0400 Sent to CCL by: "Jozsi Szegezdi" [jszegezdi+*+chemaxon.com] Dear Christos, Chemaxon's Marvin program can calculate the partial charge distribution of ionized molecules. Downloading and additional information are given at this site: http://www.chemaxon.com/product/ch_dist.html Best wishes, Jozsi From owner-chemistry@ccl.net Tue Apr 10 15:27:01 2007 From: "Elaine Meng meng|*|cgl.ucsf.edu" To: CCL Subject: CCL: Calculation of Gasteiger charges for charged molecules Message-Id: <-34016-070410152146-22421-mvqMLjMh3OyXTz5eojmBRg*_*server.ccl.net> X-Original-From: "Elaine Meng" Date: Tue, 10 Apr 2007 15:21:42 -0400 Sent to CCL by: "Elaine Meng" [meng,cgl.ucsf.edu] Hi Christos, Antechamber will calculate charges, and you have the choice of Gasteiger or more intensive methods: http://amber.scripps.edu/antechamber/ac.html The Gasteiger implementation definitely works for molecules with net charge - I just tested it on a carboxylate. You could get Antechamber on its own, or you could get Chimera, which includes Antechamber. The interface in Chimera is pretty friendly, and with Chimera you could also perform hydrogen addition before running the charge calculation. Chimera: http://www.cgl.ucsf.edu/chimera/index.html Add Charge tool (uses Antechamber for nonstandard residues): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng,cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html