From chemistry-request@server.ccl.net Tue Oct 12 09:05:19 1999 Received: from ms.dicp.ac.cn ([159.226.159.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA03183 for ; Tue, 12 Oct 1999 09:05:10 -0400 Received: from p100 ([159.226.159.123]) by ms.dicp.ac.cn (8.8.5/SCO5) with SMTP id UAA08560 for ; Tue, 12 Oct 1999 20:56:12 +0800 (CST) Message-Id: <199910121256.UAA08560@ms.dicp.ac.cn> Date: Tue, 12 Oct 1999 21:5:47 +0800 From: Li Guo Hui To: "CHEMISTRY@ccl.net" Subject: Correction of force constant? Organization: Dalian Institute of Chemical Physics X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear,CCLers: i knew little about "Correction of force constant" from others who said it exists in G94 or G98. but i dont know datails about this theme.could someone tell me something about this..thanks in advance. i would summary the answers. Best wishes with you From chemistry-request@server.ccl.net Tue Oct 12 09:05:26 1999 Received: from ms.dicp.ac.cn ([159.226.159.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA03184 for ; Tue, 12 Oct 1999 09:05:11 -0400 Received: from p100 ([159.226.159.123]) by ms.dicp.ac.cn (8.8.5/SCO5) with SMTP id UAA08565 for ; Tue, 12 Oct 1999 20:56:24 +0800 (CST) Message-Id: <199910121256.UAA08565@ms.dicp.ac.cn> Date: Tue, 12 Oct 1999 21:5:59 +0800 From: Li Guo Hui To: "CHEMISTRY@ccl.net" Subject: Correction of force constant? Organization: Dalian Institute of Chemical Physics X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear,CCLers: i knew little about "Correction of force constant" from others who said it exists in G94 or G98. but i dont know datails about this theme.could someone tell me something about this..thanks in advance. i would summary the answers. Best wishes with you From chemistry-request@server.ccl.net Tue Oct 12 09:31:06 1999 Received: from arnold.chem.uoa.gr (arnold.chem.uoa.gr [195.134.76.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA03413 for ; Tue, 12 Oct 1999 09:31:02 -0400 Received: from localhost (jkerk@localhost) by arnold.chem.uoa.gr (8.8.8/8.8.8) with SMTP id QAA13513; Tue, 12 Oct 1999 16:17:40 +0300 (EET DST) Date: Tue, 12 Oct 1999 16:17:39 +0300 (EET DST) From: John Kerkines Reply-To: John Kerkines To: chminf-l@listserv.indiana.edu, chemistry@ccl.net, chemweb@ic.ac.uk cc: orglist@dq.fct.unl.pt Subject: Nobel Prize in Chemistry 1999 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sorry for the duplicate postings The Nobel Committee just announced that the Nobel Prize in Chemistry 1999 is awarded to Professor Ahmed H. Zewail from Caltech for his studies of the transition states of chemical reactions using femtosecond spectroscopy. For more info http://www.nobel.se/announcement-99/chemistry99.html Regards, John Kerkines Athens, Greece From chemistry-request@server.ccl.net Tue Oct 12 15:27:34 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 PAA04800 for ; Tue, 12 Oct 1999 15:27:34 -0400 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id PAA26250 for ; Tue, 12 Oct 1999 15:22:24 -0400 (EDT) Received: (from daemon@localhost) by bioc1.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id MAA15833 for ; Tue, 12 Oct 1999 12:22:45 -0700 (PDT) Received: from dxg-pc.msi.com(146.202.11.19) by bioc1.msi.com via smap (V2.0) id xma015827; Tue, 12 Oct 99 12:22:35 -0700 Message-Id: <3.0.32.19991012121824.00938d20@146.202.6.130> X-Sender: dgregory@146.202.6.130 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Tue, 12 Oct 1999 12:18:24 -0700 To: chemistry@ccl.net (Comp. Chem. List) From: Don Gregory Subject: Re: [charmm-bbs] H-bond parameters (2) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" 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 From chemistry-request@server.ccl.net Tue Oct 12 22:42:28 1999 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA06415 for ; Tue, 12 Oct 1999 22:42:28 -0400 Received: from localhost (kuwata@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id TAA24138 for ; Tue, 12 Oct 1999 19:45:11 -0700 (PDT) X-Authentication-Warning: neon.chem.ucla.edu: kuwata owned process doing -bs Date: Tue, 12 Oct 1999 19:45:11 -0700 (PDT) From: Keith Kuwata To: chemistry@server.ccl.net Subject: MOLCAS/GUGA question (again) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers, I am still struggling to do MRCI via MOLCAS. Since a full CI is impossible, I want to use a set of reference configurations. For one of the species I want to study, the configurations with CI coefficient > 0.05 are conf/sym 11111 Coeff Weight 2 2u200 -.60995 .37203 6 2udu0 -.43099 .18575 16 2uud0 .24891 .06196 22 2u020 .60850 .37027 53 0u202 -.06125 .00375 74 0u022 .06111 .00373 My question is, how do I specify u(p) vs. d(own) in my guga input deck? I will summarize any responses. Thanks for your help, Keith Kuwata From chemistry-request@server.ccl.net Tue Oct 12 22:47:07 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 WAA06447 for ; Tue, 12 Oct 1999 22:47:07 -0400 Received: from kitts.u.arizona.edu (fan@kitts.U.Arizona.EDU [128.196.137.17]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id WAA00444 for ; Tue, 12 Oct 1999 22:41:52 -0400 (EDT) Received: from localhost (fan@localhost) by kitts.u.arizona.edu (8.8.8/8.8.8) with ESMTP id TAA22790 for ; Tue, 12 Oct 1999 19:41:53 -0700 Date: Tue, 12 Oct 1999 19:41:53 -0700 (MST) From: Hua-Jun Fan To: chemistry@ccl.net Subject: "conspiring" theory In-Reply-To: <47F7EAA0389AD011840500805FEAB9C60376E31A@sctms01.sct.ucarb.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, CCLers I wonder if anyone on this list have seen/read any papers about "conspiring" theory. To my understanding, the theory states that in the transition metal complexes, the combination of multiple ligand orbitals can provide better interaction with metal than a single ligand orbital does. For example, nitrosyl is a good backbonding ligand with metal. With appropriate symmetry, the combination of (pi)* orbital of dinitrosyl can be even stronger backbonding ligand because the combinated orbital lows its energy from single NO and close to Metal orbitals. Best regards! Huajun