From chemistry-request@server.ccl.net Tue Oct 12 10:29:41 1999 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA03643 for ; Tue, 12 Oct 1999 10:29:41 -0400 Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.20.129]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id KAA23997; Tue, 12 Oct 1999 10:24:04 -0400 Sender: richard@tc.cornell.edu Message-ID: <38034484.2781@tc.cornell.edu> Date: Tue, 12 Oct 1999 10:24:04 -0400 From: Richard Gillilan X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: Pieter Stouten CC: chemistry@ccl.net Subject: Re: CCL:PLP - piecewise linear potential? References: <0010CDA3.C21441@eu.pnu.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Ooops, thanks for catching that! My apologies to the FlexX folks (http://cartan.gmd.de/flexx/html/about_flexx.html). Richard Pieter Stouten wrote: > > Hello Richard, > > >FlexX (Luty, Wasserman, Stouten and Hodge) > >J. Comp. Chem. Vol 16, No 4 454-464 (1995) > > > Thanks for crediting FlexX to us, but it is Rarey's & Lengauer's. The > docking tool referred to in the above paper is known under various > names: BForce, GridDocking and (MSI's version) Affinity. > > Ciao, > > Pieter > > Pieter F.W. Stouten, Ph.D. > Head, Computational Chemistry > Discovery Research Oncology > Pharmacia & Upjohn > Viale Pasteur 10 > 20014 Nerviano (Mi) > Italy From chemistry-request@server.ccl.net Tue Oct 12 12:15:15 1999 Received: from tech.chem.ethz.ch (ltcmail.ethz.ch [129.132.124.253]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA04122 for ; Tue, 12 Oct 1999 12:15:14 -0400 Received: from tech.chem.ethz.ch (baiker8.ethz.ch [129.132.125.8]) by tech.chem.ethz.ch (8.8.8/8.8.8) with ESMTP id SAA14298 for ; Tue, 12 Oct 1999 18:10:09 +0200 (CEST) Message-ID: <38036ACB.BA6F4E04@tech.chem.ethz.ch> Date: Tue, 12 Oct 1999 19:07:23 +0200 From: angelo vargas Organization: ETHZ X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: basis set for Nickel Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Can anybody suggest a good basis set for Nickel ( Gaussians )? I am having problems with the convergence of Ni complexes with Gaussian 98 using a 6-31G** basis set. Any suggestions are welcome. Angelo _______________________________________________________________________ Angelo Vargas Laboratory of Technical Chemistry Department of Chemical Engineering and Industrial Chemistry Swiss Federal Institute of Technology (ETHZ) ETH Zentrum, Universitätsstr. 6 Telefon: 0041/1/632 31 54 CH-8092 Zürich - Switzerland Fax: 0041/1/632 11 63 E-mail: vargas@tech.chem.ethz.ch http://mercury.ethz.ch/members/vargas/vargas.html ________________________________________________________________________ From chemistry-request@server.ccl.net Tue Oct 12 15:38:30 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA04876 for ; Tue, 12 Oct 1999 15:38:30 -0400 Received: from cbdcom-emh1.apgea.army.mil (cbdcom-emh1.apgea.army.mil [131.92.10.15]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id PAA27004 for ; Tue, 12 Oct 1999 15:32:53 -0400 (EDT) Received: by cbdcom-emh1.apgea.army.mil with Internet Mail Service (5.5.2448.0) id <4T2QC295>; Tue, 12 Oct 1999 15:27:06 -0400 Message-ID: <6E9332894560D211ADA700104B6968EA012EF36D@netsvr1> From: "Famini George R Dr. SBCCOM" To: "'chemistry@ccl.net'" Subject: COMP Association with JMGM Date: Tue, 12 Oct 1999 15:30:16 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id PAA04877 There have been several comments and concerns recently with respect to Don Boyd's recent email posting regarding the American Chemical Society's Division of Computers in Chemistry's relationship with the Elsevier, and in particular, the Journal of Molecular Graphics and Modeling (JMGM), Although I have responded in the past to some concerns, I felt it was important to elucidate precisely what the relationship is regarding JMGM and COMP, as well as the rationale to why the COMP Executive Committee entered into this agreement with Elsevier. The agreement between COMP and JMGM was developed over an 18 month period, concluding about a year ago. It was felt by the COMP Executive Committee that current ACS journals to do not adequately address all of areas of interest of COMP members, and that an association was needed with another journal. Elsevier approached the Executive Committee with an offer for COMP to actively participate in the "rebirth" of the JMGM. Further, the JMGM, through the incorporation of Chemical Design News, would give COMP a mechanism to "advertise" upcoming events, symposia and meetings of interest to COMP members. The actual terms of the agreement provide: 1) a non-exclusive association between COMP and JMGM. This means that JMGM is A journal of COMP, not THE journal. This gives COMP maximum flexibility to develop similar relationships with other journals that may further address the needs of the COMP members. The fact is, however, no other journal as sought to establish the same relationship with us (but more on that below). 2) COMP members receive a substantial discount when subscribing to JMGM. 3) The COMP Executive Board was allowed to select, with Elsevier's concurrence, the North American Editor of JMGM. As a recognition of this tie, the COMP Executive Board has included the North American editor as an ex-officio, non-voting member of the Executive Board. I feel this solidifies the relationship between the JMGM and COMP, and really does give us the opportunity to influence how the journal is being run. A case in point recently was the selection of the editor of the Chemical Design Automation and News pages: the COMP Executive Committee was solicited for recommendations. 4) COMP would agree to encourage appropriate papers be published in JMGM. This raised a very lengthy discussion vis-à-vis symposia papers, and where the right spot for publication was: JMGM, JCICS or symposium series books. It was decided that there were ample opportunities that there would not be a detrimental effect on any of the three, and that we were free to recommend publication to the most appropriate journal/book. I feel it is important to note that this arrangement with the JMGM does not entail any financial obligation on COMP's part, nor does it commit COMP to support JMGM exclusive to any other journal/opportunity. During the negotiations and discussions with Elsevier, the Executive Committee felt it was important not to exclude JCICS in the discussions, as they, after all, are and ACS journal. We felt that it was important for JCICS to understand what was being considered between JMGM and COMP, give them an opportunity to express concerns, and more importantly, give them an opportunity to enter into an analogous arrangement. I think it is important at this point to mention that that is no official relationship between JCICS and COMP. JCICS is not in any way associated with COMP, other than the relationship with ACS. As such, JCICS is not an official journal of COMP. However, the Executive Committee does realize that JCICS has attempted to serve the computational chemistry community, but felt that it had neither the readership nor the reputation in computational chemistry to adequately to do so. COMP was not party to an attempt to subvert JCICS to purely computational chemistry. This was an initiative that came out of ACS Pubs. The editor of JCICS felt comfortable with the current relationship between JCICS and COMP (which is to say, none), and with the relationship between JMGM and COMP. For those "naysayers" that claim JCICS does computational chemistry, I should note that my laboratory cancelled their subscription to JCICS because it did not meet our needs in the computational chemistry area. Further, when I have perused journal, I find the number of "information" based papers far outweighing the computational papers. The COMP Executive Committee felt then, and continues to feel, that JCICS does not adequately represent the key areas in which COMP is engaged. Further, JCICS leadership did not feel obligated to include COMP in the process of attempting to do so. For these reasons, we voted for, and approved, the aforementioned relationship with JMGM. However, COMP is willing to consider an analogous relationship with any other journal that feels an "official" relationship with COMP. To restate the advantages of this relationship to COMP members: a) Reduced prices for an important journal in computational chemistry b) Ability for COMP to influence the editorial content to address COMP members' interests c) Excellent venue for publication of members' papers, including full color at no charge d) Increased exposure of COMP symposia and events e) Enhanced international presence of COMP, as JMGM has a worldwide readership Finally, our association with Elsevier was coordinated with ACS, and the contract was concluded only after they raised no objections. I hope this adequately addresses recent concerns. The COMP Executive Board is always willing to discuss this with anyone with legitimate questions. George Famini COMP Division Chair George R. Famini, PhD Chief, International Programs Office ECBC/SBCCOM (410)436-2552 fax: (41)436-5373 From chemistry-request@server.ccl.net Tue Oct 12 18:43:36 1999 Received: from smtp04.nwnexus.com (smtp04.nwnexus.com [206.63.63.52]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA05559 for ; Tue, 12 Oct 1999 18:43:35 -0400 Received: from oemcomputer (blv-pm408-ip57.nwnexus.net [206.63.37.57]) by smtp04.nwnexus.com (8.8.8/8.8.8) with SMTP id PAA18158 for ; Tue, 12 Oct 1999 15:38:20 -0700 (PDT) Message-ID: <007901bf1503$06c19ba0$39253fce@oemcomputer> From: "Gina Miller" To: Subject: Re: CCL:Question About Structure/Viewing Software Date: Tue, 12 Oct 1999 15:42:11 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Also try RasMol (free) http://cbr.nc.us.mensa.org/homepages/RayLec/rasmol.htm And Chemscape Chime: (free) http://www.hotwired.com/webmonkey/pluginpack/chemscape.html And VRML Gina "Nanogirl" Miller Nanotechnology Industries http://www.nanoindustries.com nanogirl@halcyon.com >Rolf Claessen [mailto:administration@claessen.net] wrote: > >> for >> visualization I >> would recommend the free program swissPDB in combination with >> POV Ray (also >> free and maybe the best raytracer). > >I find that WebLabViewer Lite (free from MSI, http://www.msi.com) also >generates nice pictures of smaller molecules and is easy to use. > >HTH > >Dr Tom Hawkins Osmetech plc From chemistry-request@server.ccl.net Tue Oct 12 11:07:09 1999 Received: from mail.bucknell.edu (marge.bucknell.edu [134.82.9.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA03857 for ; Tue, 12 Oct 1999 11:07:09 -0400 Received: from williams.bucknell.edu (williams.bucknell.edu [134.82.59.42]) by mail.bucknell.edu (8.9.3/8.9.3) with SMTP id LAA09581 for ; Tue, 12 Oct 1999 11:02:06 -0400 (EDT) Date: Tue, 12 Oct 1999 11:02:06 -0400 (EDT) Message-Id: <199910121502.LAA09581@mail.bucknell.edu> X-Sender: williams@mail.bucknell.edu X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: Brian Williams Subject: Diatomic Potential Energy Curves My apologies for what is probably a naive question. When I read texts on computational chemistry/quantum chemistry, I often see for H2 potential energy curves comparing the simpler theoretical treatments with the "experimental" energy curve (eg Karplus and Porter, "Atoms and Molecules", p 290), the point being that the theoretical treatment always gives a higher value. My question is, where can I find these experimental potential energy values as a function of distance for simple diatomics like H2? I know of references such as Herzberg where equilibrium distances, energies and force constants are given, but these only cover one point on the curve. Is there a general compilation of potential energy curve data for diatomics? Thanks. Brian Williams, Chemistry Bucknell University From chemistry-request@server.ccl.net Wed Oct 13 05:24:02 1999 Received: from c008.sfo.cp.net (c008-h017.c008.sfo.cp.net [209.228.14.206]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA08587 for ; Wed, 13 Oct 1999 05:24:01 -0400 Message-Id: <199910130924.FAA08587@server.ccl.net> Received: (cpmta 12542 invoked from network); 13 Oct 1999 02:18:45 -0700 Received: from pcb4122.univ-lemans.fr (193.52.30.155) by smtp.cristal.org with SMTP; 13 Oct 1999 02:18:45 -0700 X-Sent: 13 Oct 1999 09:18:45 GMT X-Sender: pop@mail.cristal.org X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Wed, 13 Oct 1999 11:17:57 +0200 To: From: Armel Le Bail Subject: Re: CCL:Question About Structure/Viewing Software Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 15:42 12/10/99 -0700, Gina Miller wrote: >Also try RasMol (free) >http://cbr.nc.us.mensa.org/homepages/RayLec/rasmol.htm > >And Chemscape Chime: (free) >http://www.hotwired.com/webmonkey/pluginpack/chemscape.html > >And VRML > Have a look at the CCP14 pages about structure drawing : http://www.ccp14.ac.uk/solution/structuredrawing/index.html And for VRML as related to crystallography, see : http://sdpd.univ-lemans.fr/vrml/intvrml.html Armel Le Bail http://sdpd.univ-lemans.fr/course/ From chemistry-request@server.ccl.net Wed Oct 13 11:51:12 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA11529 for ; Wed, 13 Oct 1999 11:51:12 -0400 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id LAA08120 for ; Wed, 13 Oct 1999 11:45:50 -0400 (EDT) Received: from urbana.ks.uiuc.edu (urbana.ks.uiuc.edu [130.126.120.125]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with SMTP id KAA07733 for ; Wed, 13 Oct 1999 10:45:44 -0500 (CDT) Message-Id: <199910131545.KAA07733@havana.ks.uiuc.edu> Date: Wed, 13 Oct 1999 10:45:43 -0500 (CDT) From: Dorina Kosztin Reply-To: Dorina Kosztin Subject: HOLE program To: CHEMISTRY@www.ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: 4jjaEDRD+Irufw3EYCE4Xw== X-Mailer: dtmail 1.3.0 CDE Version 1.3 SunOS 5.7 sun4u sparc I would greatly appreciate if somebody could tell me where I can get the program HOLE (Smart et al. 1993) from. Thank you, Dorina Kosztin --------------------------------------------------------- Theoretical Biophysics Group Email: dorina@ks.uiuc.edu Beckman Institute, UIUC Phone: (217) 244-8946 405 North Mathews Ave. Fax: (217) 244-6078 Urbana, IL 61801, USA http://www.ks.uiuc.edu/ --------------------------------------------------------- From chemistry-request@server.ccl.net Wed Oct 13 12:05:57 1999 Received: from york.ac.uk (pump3.york.ac.uk [144.32.128.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA11692 for ; Wed, 13 Oct 1999 12:05:56 -0400 Received: from york.ac.uk (joker.chem.york.ac.uk [144.32.180.45]) by york.ac.uk (8.9.3/8.9.3) with ESMTP id QAA29732 for ; Wed, 13 Oct 1999 16:58:32 +0100 (BST) Sender: meike@york.ac.uk Message-ID: <3804AD16.58C52F9F@york.ac.uk> Date: Wed, 13 Oct 1999 17:02:30 +0100 From: Meike Reinhold X-Mailer: Mozilla 4.7 [en] (X11; I; AIX 4.2) X-Accept-Language: en MIME-Version: 1.0 To: chemistry Subject: symmetry in G98 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit HI All, I have asked this question already some time ago, but I am still not totally clear about the use of symmetry in Gaussian. Maybe somebody would be so nice to point me to a good reference or so. The question is: I want to calculate the geometry and the frequencies of a highly symmetric molecule (in this case D6H). The variables have been chosen in order to be D6H, this means the bond length, etc. which generate the symmetry have all the same variable. If I use only the default input without the symmetry keyword, than G98 recognizes the symmetry, but during the optimization it aborts the calculation because the molecule has no longer D6H symmetry (this is what I make out from the error message). Symmetry saves time and helps in a lot of ways. COuld somebody explain me what exactly happens in simple words? Thanks, Meike Reinhold Ph.D. Student Chemistry Department York University UK From chemistry-request@server.ccl.net Wed Oct 13 12:28:23 1999 Received: from server2.seas.ucla.edu (Server2.seas.ucla.edu [128.97.10.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA11794 for ; Wed, 13 Oct 1999 12:28:23 -0400 Received: from indium (Indium.seas.ucla.edu [128.97.83.8]) by server2.seas.ucla.edu (8.8.8/8.8.8(SEAS.0002)) with SMTP id JAA22930 for ; Wed, 13 Oct 1999 09:23:02 -0700 Reply-To: From: "Qiang Fu" To: Subject: RE: symmetry in G98 Date: Wed, 13 Oct 1999 09:15:17 -0700 Message-ID: <000001bf1596$23cd5480$08536180@indium.seas.ucla.edu> 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 8.5, Build 4.71.2173.0 Importance: Normal In-Reply-To: <3804AD16.58C52F9F@york.ac.uk> X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear Meike Reinhold, I had the similar problem before. During the optimization, G98 tries to change the orientation of the molecule, which results abnormal ending of the calculation. Thanks to Dmitry from Emory, I can overcome this problem now. I hope the email from Dmitry will be helpful to you. later Qiang Fu -----Original Message----- From: Dmitry Khoroshun [mailto:dima@euch4e.chem.emory.edu] Sent: Sunday, May 02, 1999 10:26 PM To: fuq@ucla.edu Subject: symmetry Hello! I suggest you explore Gaussian's IOP's. They are available in Technical information on www.gaussian.com . Particularly, you may want to set iop(2/16=2) or iop(2/16=3), which governs what happens when the group or orientation changes (default is to bomb off). Also, you may want to increase the difference criteria determining is structure is symmetric (iops 2/17 and 2/18). Sincerely, Dmitry Khoroshun dima@euch4e.chem.emory.edu HI All, I have asked this question already some time ago, but I am still not totally clear about the use of symmetry in Gaussian. Maybe somebody would be so nice to point me to a good reference or so. The question is: I want to calculate the geometry and the frequencies of a highly symmetric molecule (in this case D6H). The variables have been chosen in order to be D6H, this means the bond length, etc. which generate the symmetry have all the same variable. If I use only the default input without the symmetry keyword, than G98 recognizes the symmetry, but during the optimization it aborts the calculation because the molecule has no longer D6H symmetry (this is what I make out from the error message). Symmetry saves time and helps in a lot of ways. COuld somebody explain me what exactly happens in simple words? Thanks, Meike Reinhold Ph.D. Student Chemistry Department York University UK -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Oct 13 03:22:33 1999 Received: from alchemy.yonsei.ac.kr (alchemy.yonsei.ac.kr [165.132.31.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA07904 for ; Wed, 13 Oct 1999 03:22:29 -0400 Received: from ldw.yonsei.ac.kr (ldw.yonsei.ac.kr [165.132.31.51]) by alchemy.yonsei.ac.kr (8.8.8H2/8.8.8) with SMTP id QAA29637 for ; Wed, 13 Oct 1999 16:16:29 +0900 (KST) Message-ID: <001501bf154d$22455f20$331f84a5@yonsei.ac.kr> From: To: "ccl" Subject: molecular docking program??? Date: Wed, 13 Oct 1999 16:32:40 +0900 Dear everyone!!!! Does anyone know of a molecular docking program? That is program properity, web site, commercial price(academic) and accuracy of theory. Docking molecular number is carbon 20, nitrogen 5 and oxygen 5. Total molecular number is 50. It's a small two molecular. I'm looking for general docking program. I working workstation, win NT and window98. I'm not want "Run on SGI". I'll favor your answer.----------------------------------Thank's everyone. ----------------------------------------------------------------------- Young Jae Park Ph. D Student Analytical Chemistry E-mail geniyjp@alchemy.yonsei.ac.kr , geniyjp@hanmail.net Address Dept.of Chem., Yonsei Univ. Seoul, 120-749, S. Korea Tel 82-2-361-2635 Fax 82-2-364-7050 ----------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Oct 13 13:31:36 1999 Received: from xray5.chem.louisville.edu (xray5.chem.louisville.edu [136.165.12.18]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA12175 for ; Wed, 13 Oct 1999 13:31:35 -0400 Received: (from dew01@localhost) by xray5.chem.louisville.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id NAA08993 for chemistry@ccl.net; Wed, 13 Oct 1999 13:26:09 -0400 From: "Donald E. Williams" Message-Id: <9910131326.ZM8991@xray5.chem.louisville.edu> Date: Wed, 13 Oct 1999 13:26:09 -0400 In-Reply-To: Don Gregory "CCL:[charmm-bbs] H-bond parameters (2)" (Oct 12, 12:18pm) References: <3.0.32.19991012121824.00938d20@146.202.6.130> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@ccl.net Subject: How are H-bonds parameterized in force fields? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii A common way of parameterizing the H-bond in force fields is just to ignore nonbonded interactions of hydrogen bonded to e.g. O or N; that is, all nonbonded exchange repulsion and dispersion attraction of H-bonded hydrogen are arbitrarily set to zero. This is called the "disappearing hydrogen" model. Coulombic energy (usually from net atomic charges) is retained. It is not correct to conclude, from the success of the disappearing hydrogen model, that H-bonds are primarily determined by coulombic interaction of net atomic charges. In the disappearing hydrogen model, H-bond energy is, by default, assumed to be the negative of a normal nonbonded hydrogen interaction. To find the H-bond energy assigned by a force field, do a separate calculation in which H bonded to e.g. O or N has the same parameters as H bonded to C. This will normally give a large positive energy, compared to the negative energy given by the disappearing hydrogen model. The difference between these two energies is the H-bond energy assigned by that force field. Tests have been made (for example J. Comp. Chem. 1993, 14, 1066) which compare energetic and structural effects of the disappearing hydrogen model. These tests show that coulombic interaction between net atomic charges (i. e., what is often called the electrostatic energy of the H-bond) is a quite minor effect, compared to the major effect of zeroing out the nonbonded interaction of H in an H-bond. The bottom line is that the H-bond is *not* primarily a coulombic effect between net atomic charges. The H-bond occurs primarily because of reduction of normal repulsion between closed shell molecules, as is normally dictated by the Pauli principle. When a normal bond forms, at least one of the entities is not closed shell. It is not clear to me why this apparent violation of the Pauli principle is allowed for the H-bond. But since a bonding-like reduction of repulsion does occur, the H-bond can be classified as a weak (but very important) polar covalent bond. On Oct 12, 12:18pm, Don Gregory wrote: > Subject: CCL:[charmm-bbs] H-bond parameters (2) > Hi Lesley, > I'm glad you asked these two questions, because they point out some > important aspects I was trying to make in my earlier response. > > Empirical force fields can *only* calculate those energy term they are > parameterized for, so if you are using a force-field that wasn't > parameterized using an explicit H-Bond term, it would be an inappropriate > question to ask "what is the H-Bond component". > > To ask this question, you'd have to use a force-field that was > parameterized using explicit H-Bonding terms (which would no doubt > have other parameters different [e.g. electrostatics and vdW]) > > You can 'approximate' the strength of the H-Bonds by 'turning them on' > (i.e. incr. cuthb) but these numbers should *not* be relied upon too > greatly, since, again, those values were not used in the force-field > optimization. They are probably hold-overs from earlier optimizations > when they were included explicitly. > > As for 'what do you do when there are no H-Bond terms in the force-field' > (even if you are using a field that has explicit H-Bond terms); the answer > there > is the same as any 'missing parameter' problem, i.e. you'd need to search > the literature to see if anyone has optimized such a parameter *using* the > same force-field you are using. > > The script I provided still works with a Cys present, but you're right, > since there are not terms to calculate, one cannot even analyze for > H-Bond geometries (which is the recommended use of the H-Bond > commands I gave; also Lennart Nilsson reminded us of the > "coor hbond" command which helps with analysis w/o the use of > the force-field parameters). > > DG > > > At 04:25 PM 10/11/1999 +0100, you wrote: > >Thank you all for your help regarding my recent question on H-bond > >parameters. Following on from everything that has been said I would like > >to ask two more questions: > > > >(1) If hydrogen bonding is implicit in electrostatics and vdW terms, how > >do you analyse the energy term to find the contribution to energy which > >is due to hydrogen bonding? I assume this is a valid occasion for using > >HBONDS > > > >(2) If you determine the energy due to hydrogen bonds using HBONDS CUTHB > >4.5 (for example), how do you account for sulfur containing systems, > >particularly cysteine residues, when sulfur is not parameterised in the > >HBOND section of the parameter file? > > > >If you run the script that Don Gregory sent to the list, but replace one > >of the residues with CYS this adapted script falls over because there > >are no hydrogen bond parameters. > > > >Thanks again for your help so far. Look forward to hearing from you > >again. > >Lesley > > Dr. Don Gregory (dgregory@msi.com) > Asia Pacific Science Liaison > Molecular Simulations Inc. > 9685 Scranton Rd. > San Diego, CA 92121 > (619) 799-5331 http://www.msi.com > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >-- End of excerpt from Don Gregory -- Dr. Donald E. Williams email:dew01@xray5.chem.louisville.edu Department of Chemistry http://www.louisville.edu/~dewill01 University of Louisville phone:502-852-5975 Louisville, KY 40292 fax: 502-852-8149 From chemistry-request@server.ccl.net Wed Oct 13 13:47:00 1999 Received: from ma3.justnet.ne.jp (www3p.justnet.ne.jp [133.130.3.17]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA12346 for ; Wed, 13 Oct 1999 13:46:41 -0400 Received: (qmail 22530 invoked from network); Thu, 14 Oct 1999 02:41:02 +0900 Received: (ofmipd 133.81.144.76); Thu, 14 Oct 1999 02:41:02 +0900 Date: Thu, 14 Oct 1999 02:52:13 +0900 Message-ID: <19991014025213.1.22525.qmail@ma3.justnet.ne.jp> From: "E.Hiramatsu" To: Subject: Geometry optimization question on US Gamess. X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-2022-JP Content-Transfer-Encoding: 7bit Dear CCLers. I have a question on geometry optimization. I optimized the sturucture of 1:1 complex of hydrated Alumnum ion Al(H2O)6 with diphosphate P2O7 on USGamess. The result was expected that optimized structure was Al(H2O)5P2 but , it showed Al(H2O)3(OH)2P2 which isomer of Al(H2O)5P2. *P2O7 is expressed P2. I want to optimize the Al(H2O)5P2 complex keeping five hydrated. The follow is inputfile of gamess I used. $CONTRL ECP=SBK SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT MAXIT=300 ICHARG=-1 $END $SYSTEM MEMORY=30000000 TIMLIM=6000 $END $BASIS GBASIS=N21 NGAUSS=3 NDFUNC=2 $END $SCF DIRSCF=.TRUE. DAMP=.TRUE. FDIFF=.FALSE. $END $INTGRL NOPK=1 $END $STATPT NSTEP=40000 $END $DATA Please some suggestion me. Thanks. Eishi Hiramatsu Department of Chemistry, Fukuoka University of Education Senior student of MC From chemistry-request@server.ccl.net Wed Oct 13 16:06:05 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA13323 for ; Wed, 13 Oct 1999 16:06:05 -0400 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id QAA13896 for ; Wed, 13 Oct 1999 16:00:39 -0400 (EDT) Received: from venezia.ks.uiuc.edu (IDENT:barryi@venezia.ks.uiuc.edu [130.126.120.96]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id PAA10016; Wed, 13 Oct 1999 15:00:41 -0500 (CDT) Received: (from barryi@localhost) by venezia.ks.uiuc.edu (8.8.7/8.6.9)id QAA22459; Wed, 13 Oct 1999 16:00:48 -0400 From: Barry Isralewitz Message-Id: <199910132000.QAA22459@venezia.ks.uiuc.edu> Subject: Re: CCL:HOLE program To: dorina@ks.uiuc.edu (Dorina Kosztin) Date: Wed, 13 Oct 1999 15:00:48 -0500 (CDT) Cc: CHEMISTRY@www.ccl.net In-Reply-To: <199910131545.KAA07733@havana.ks.uiuc.edu> from Dorina Kosztin at "Oct 13, 99 10:45:43 am" X-Mailer: ELM [version 2.4ME+ PL15 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi Dorina, > I would greatly appreciate if somebody could tell me where I can get the program > HOLE (Smart et al. 1993) from. Looks like the site for HOLE: A Program for the Analysis of the Pore Dimensions of Ion Channel Structural Models [J. Mol. Graphics., (1996) 14, 354-360., Smart et al.] (note they use this different reference on their site) is http://www.biochemistry.bham.ac.uk/osmart/hole/ Barry --- Barry Isralewitz Theoretical Biophysics Group Beckman 3121 Office Phone: (217) 244-1612 Home Phone: (217) 337-6364 email: barryi@ks.uiuc.edu http://www.ks.uiuc.edu/~barryi From chemistry-request@server.ccl.net Wed Oct 13 17:24:19 1999 Received: from ChE.UDel.Edu (che.udel.edu [128.175.117.64]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA13895 for ; Wed, 13 Oct 1999 17:24:19 -0400 Received: from che.udel.edu (IDENT:sum@entropy.che.udel.edu [128.175.117.58]) by ChE.UDel.Edu (8.9.3/8.9.3) with ESMTP id RAA18894 for ; Wed, 13 Oct 1999 17:18:55 -0400 (EDT) Sender: sum@che.udel.edu Message-ID: <3804F894.697469FA@che.udel.edu> Date: Wed, 13 Oct 1999 17:24:36 -0400 From: "Amadeu K. Sum" Organization: University of Delaware X-Mailer: Mozilla 4.7 [en] (X11; U; Linux 2.2.5-15 i686) X-Accept-Language: en, pt-BR, zh MIME-Version: 1.0 To: chemistry@ccl.net Subject: Optimization with density constrain Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear colleagues, I have come across a problem and I was wondering whether anyone knows a possible solution. I am looking for ways to perform an optimization of molecular clusters (containing several molecules) at the ab initio level such that there would be some kind of density constrain imposed in the packing of the molecule. Would anyone know of a method/algorithm/reference to such problem? Thanks in advance for any reply. Amadeu Email: sum@udel.edu From chemistry-request@server.ccl.net Wed Oct 13 17:59:17 1999 Received: from mgcct6.nci.nih.gov (mgcct6.nci.nih.gov [137.187.211.216]) by server.ccl.net (8.8.7/8.8.7) with SMTP id RAA14047 for ; Wed, 13 Oct 1999 17:59:16 -0400 Received: from helix.nih.gov (localhost [127.0.0.1]) by mgcct6.nci.nih.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id UAA02567 for ; Wed, 13 Oct 1999 20:03:53 -0400 Sender: brunob@helix.nih.gov Message-ID: <38051DE8.6DE2AC0@helix.nih.gov> Date: Wed, 13 Oct 1999 20:03:52 -0400 From: Bruno Bienfait Organization: National Cancer Institute X-Mailer: Mozilla 4.6 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Computer Chemistry List Subject: Tanimoto coefficient algorithm Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id RAA14048 Dear CCL, I am looking for a fast algorithm to compute the Tanimoto coefficient . Any references or pointers to source code would be welcome. Thanks in advance Bruno Bienfait -- [ Bruno Bienfait, Ph. D. Laboratory of Medicinal Chemistry ] [ National Cancer Institute ] [ Email : brunob@helix.nih.gov National Institutes of Health ] [ Phone : (301) 402-3111 Building 37, Room 5B20 ] [ Fax : (301) 496-5839 Bethesda Maryland 20892 , USA ] [ WWW : http://www.brunob.org ]