From owner-chemistry@ccl.net Sun Oct 9 07:24:00 2005 From: "Dr Seth Olsen s.olsen1!A!uq.edu.au" To: CCL Subject: CCL: AMBER parameters for uncharged N-terminus Message-Id: <-29521-051009060937-28281-4QkiKnl5fBkbcGKRXCmRWA++server.ccl.net> X-Original-From: Dr Seth Olsen Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Sun, 09 Oct 2005 20:09:24 +1000 MIME-Version: 1.0 Sent to CCL by: Dr Seth Olsen [s.olsen1^_^uq.edu.au] Hi CCLers, I am curious if anybody knows of an available set of AMBER parameters for uncharged N-terminus amino acid residues. Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1()uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms From owner-chemistry@ccl.net Sun Oct 9 11:32:00 2005 From: "JunJun Liu ljjlp03-x-gmail.com" To: CCL Subject: CCL: How to get depolarization ratios values? Message-Id: <-29522-051009112209-30116-YnMH7SrytD1H++CQ9PnXyA|-|server.ccl.net> X-Original-From: "JunJun Liu" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=utf-8 Date: Sun, 09 Oct 2005 22:32:44 +0800 MIME-Version: 1.0 Sent to CCL by: "JunJun Liu" [ljjlp03:_:gmail.com] Dear CCLs: I knew from the test cases that doing freq calculation with G03 will get the depolarization ratios. However, when I perform a freq calculation on CH3CN with G03, there's no any depoloarization ratios produced. For example: ---------- Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), depolarization ratios for plane and unpolarized incident light, reduced masses (AMU), force constants (mDyne/A), and normal coordinates: 1 2 3 A" A' A' Frequencies -- 281.7028 281.9966 757.9365 Red. masses -- 3.5410 3.5427 6.5229 Frc consts -- 0.1656 0.1660 2.2078 IR Inten -- 0.0021 0.0021 4.8066 Atom AN X Y Z X Y Z X Y Z 1 6 0.00 0.00 0.40 0.41 0.00 0.00 0.00 0.26 0.00 2 7 0.00 0.00 -0.23 -0.23 0.00 0.00 0.00 0.34 0.00 3 6 0.00 0.00 -0.06 -0.06 0.00 0.00 0.00 -0.55 0.00 4 1 -0.01 -0.51 -0.29 -0.30 0.29 -0.01 -0.02 -0.41 0.04 ---------- As can be seen, only depolarization rasios lost. I'm wondering why does this happen and how to perform a depoloarzation ratios calculation. Any help will be highly appreciated! Here is my input file: ---------- #p b3lyp/6-31g opt freq Title Card Required 0 1 C 0 8.200000 0.000000 -9.250000 N 0 8.200000 0.000000 Z1 C 0 X1 0.000000 Z2 H 0 X2 Y1 Z3 H 0 X3 Y2 Z4 H 0 X4 Y3 Z5 Z1 -8.090000 Z2 -10.790000 Z3 -11.146666 Z4 -11.146666 Z5 -11.146667 X1 8.200000 X2 8.704403 X3 8.704403 X4 7.191194 Y1 0.873652 Y2 -0.873652 Y3 0.000000 ----------- Best Regards! Liu -- JunJun Liu College of Chemistry Central China Normal University WuHan 430079 P.R. China From owner-chemistry@ccl.net Sun Oct 9 13:20:00 2005 From: "zborowsk^chemia.uj.edu.pl" To: CCL Subject: CCL: How to get depolarization ratios values? Message-Id: <-29523-051009131707-30791-aMkNXv3htusr6T1unkjBag=-=server.ccl.net> X-Original-From: zborowsk ~ chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-2 Date: Sun, 9 Oct 2005 19:16:40 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: zborowsk..chemia.uj.edu.pl Dear JunJun Liu Not only depolarization ratios vanished, also Raman Activities. If you want to obtain Raman data for DFT methods you must use Freq=Raman option in your input Raman data are not calculated for DFT methods by default Best regards Kzys > > Sent to CCL by: "JunJun Liu" [ljjlp03:_:gmail.com] > Dear CCLs: > > I knew from the test cases that doing freq calculation with G03 will get > the depolarization ratios. However, when I perform a freq calculation > on CH3CN with G03, there's no any depoloarization ratios produced. For > example: > ---------- > Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman > scattering activities (A**4/AMU), depolarization ratios for plane and > unpolarized incident light, reduced masses (AMU), force constants > (mDyne/A), and normal coordinates: > 1 2 3 > A" A' A' > Frequencies -- 281.7028 281.9966 > 757.9365 Red. masses -- 3.5410 3.5427 > 6.5229 Frc consts -- 0.1656 0.1660 > 2.2078 IR Inten -- 0.0021 0.0021 > 4.8066 Atom AN X Y Z X Y Z > X Y Z > 1 6 0.00 0.00 0.40 0.41 0.00 0.00 0.00 0.26 > > 0.00 > 2 7 0.00 0.00 -0.23 -0.23 0.00 0.00 0.00 0.34 > > 0.00 > 3 6 0.00 0.00 -0.06 -0.06 0.00 0.00 0.00 -0.55 > > 0.00 > 4 1 -0.01 -0.51 -0.29 -0.30 0.29 -0.01 -0.02 -0.41 > > 0.04 > ---------- > As can be seen, only depolarization rasios lost. I'm wondering why does > this happen and how to perform a depoloarzation ratios calculation. Any > help will be highly appreciated! > > Here is my input file: > ---------- > #p b3lyp/6-31g opt freq > > Title Card Required > > 0 1 > C 0 8.200000 0.000000 -9.250000 > N 0 8.200000 0.000000 Z1 > C 0 X1 0.000000 Z2 > H 0 X2 Y1 Z3 > H 0 X3 Y2 Z4 > H 0 X4 Y3 Z5 > > Z1 -8.090000 > Z2 -10.790000 > Z3 -11.146666 > Z4 -11.146666 > Z5 -11.146667 > X1 8.200000 > X2 8.704403 > X3 8.704403 > X4 7.191194 > Y1 0.873652 > Y2 -0.873652 > Y3 0.000000 > > ----------- > > Best Regards! > > Liu > > -- > JunJun Liu > > College of Chemistry > Central China Normal University > WuHan 430079 > P.R. Chinalook > up the X-Original-From: line in the mail header.-- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk##chemia.uj.edu.pl ICQ 158385743 gg 3817259 skype kzys70 From owner-chemistry@ccl.net Sun Oct 9 14:27:00 2005 From: "Wayne Steinmetz WES04747(!)pomona.edu" To: CCL Subject: CCL: Good book on various Structure-Activity Relationship methods Message-Id: <-29524-051009142052-19869-qY0HNHHi3ag+/7wZA+t/+w]*[server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 9 Oct 2005 11:20:07 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747[#]pomona.edu] The classic is C. Hansch and A. Leo, "Exploring QSAR", American Chemical Society, 1995. If you want the tables as well as the analysis of methodology, purchase the two-volume set. ISBN 0-8412-3060-9. You will also find a discussion of QSAR in later editions of Burger's treatise on medicinal chemistry. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz ~ pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry ~ ccl.net [mailto:owner-chemistry ~ ccl.net] Sent: Saturday, October 08, 2005 7:35 AM To: Wayne Steinmetz Subject: CCL: Good book on various Structure-Activity Relationship methods Sent to CCL by: Yogesh Sabnis [ysabnis]![yahoo.com] Dear All, I would like to get suggestions about a book that describes various Structure-Activity Relationship methods. Thank you. Kind regards, Yogesh ######################## Yogesh Sabnis, PhD BMC, Box 574, Dept. Organic Pharmaceutical Chemistry Husargatan 3, Uppsala - 751 23 Sweden __________________________________ Yahoo! Music Unlimited Access over 1 million songs. Try it free. http://music.yahoo.com/unlimited/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. From owner-chemistry@ccl.net Sun Oct 9 18:34:00 2005 From: "Chris Vandyke vandyke]^[tripos.com" To: CCL Subject: CCL: Tripos Training Workshops 2005 Message-Id: <-29525-051009175235-3030-UP5Mfr8K7lAv18J3vP2grw+/-server.ccl.net> X-Original-From: "Chris Vandyke" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0012_01C5CCEC.EC21BF70" Date: Sun, 9 Oct 2005 16:17:18 -0400 MIME-Version: 1.0 Sent to CCL by: "Chris Vandyke" [vandyke||tripos.com] This is a multi-part message in MIME format. ------=_NextPart_000_0012_01C5CCEC.EC21BF70 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Tripos is pleased to remind you of the Training Workshop schedule for the remainder of 2005. These courses are designed to help you make the most efficient and productive use of your Tripos software. LIGAND-BASED MODELING FOR NEW MODELERS St. Louis, MO, USA. November 8-9, 2005 RECEPTOR-LIGAND MODELING FOR NEW MODELERS St. Louis, MO, USA. October 17-18, 2005 Edison, NJ, USA. November 8-9, 2005 DESIGNING ACTIVE LIGANDS WITH QSAR/COMFA St. Louis, MO, USA. November 10-11, 2005 Paris, France. November 15-16, 2005 DESIGNING OPTIMAL LIGANDS IN A RECEPTOR SITE Munich, Germany. October 13-14, 2005 LIGAND DOCKING St. Louis, MO, USA. October 19, 2005 Edison, NJ, USA. November 10, 2005 SYBYL PROGRAMMING LANGUAGE St. Louis, MO, USA. October 20-21, 2005 Paris, France. November 17-18, 2005 PHARMACOPHORE MODEL ANALYSIS Edison, NJ, USA. November 11, 2005 For course descriptions, pricing information and registration, please visit http://www.tripos.com/training. You may send questions concerning these Training Workshops to training..tripos.com. ============================= Chris Van Dyke, Ph.D. Director, Scientific Training Tripos, Inc. ============================= ------=_NextPart_000_0012_01C5CCEC.EC21BF70 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Tripos is pleased = to remind you of the Training Workshop schedule for the remainder of 2005. These = courses are designed to help you make the most efficient and productive use of = your Tripos software.

 

LIGAND-BASED = MODELING FOR NEW MODELERS

   = St. Louis, MO, USA. = November 8-9, 2005

 

RECEPTOR-LIGAND = MODELING FOR NEW MODELERS

   = St. Louis, MO, USA. = October 17-18, 2005

   = Edison, NJ, USA. = November 8-9, 2005

 

DESIGNING ACTIVE = LIGANDS WITH QSAR/COMFA

   = St. Louis, MO, USA. = November 10-11, 2005

   = Paris, France. November 15-16, 2005

 

DESIGNING OPTIMAL = LIGANDS IN A RECEPTOR SITE

   = Munich, Germany. October 13-14, 2005

 

LIGAND = DOCKING

   = St. Louis, MO, USA. = October 19, 2005

   = Edison, NJ, USA. = November 10, 2005

 

SYBYL PROGRAMMING = LANGUAGE

   = St. Louis, MO, USA. = October 20-21, 2005

   = Paris, France. November 17-18, 2005

 

PHARMACOPHORE MODEL = ANALYSIS

   = Edison, NJ, USA. = November 11, 2005

 

 

For course = descriptions, pricing information and registration, please visit http://www.tripos.com/training. You may send questions concerning these Training Workshops to = training..tripos.com.

 

 

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Chris Van Dyke, = Ph.D.

Director, = Scientific Training

Tripos, = Inc.

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D

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