From david@helium.ch.ntu.edu.tw Sat Feb 3 01:54:45 1996 Received: from king.cc.ntu.edu.tw for david@helium.ch.ntu.edu.tw by www.ccl.net (8.6.10/950822.1) id BAA27052; Sat, 3 Feb 1996 01:49:01 -0500 Received: from helium.ch.ntu.edu.tw ([140.112.54.237]) by king.cc.ntu.edu.tw (8.6.12/8.6.12) with SMTP id OAA10820; Sat, 3 Feb 1996 14:22:38 +0800 Received: by helium.ch.ntu.edu.tw; (5.65/1.1.8.2/24Jan96-0436PM) id AA04132; Sat, 3 Feb 1996 14:31:23 +0800 Date: Sat, 3 Feb 1996 14:31:23 +0800 From: Tsu-chien Weng Message-Id: <9602030631.AA04132@helium.ch.ntu.edu.tw> To: chemistry@www.ccl.net, heather@xhost2.tripos.com Subject: Re: CCL:Alchemy 2000 Dear Mr. Hunter: I read your message from CCL. I have used your product "Alchemy" on Mac IIfx when I were an undergraduate student. Now I own one PowerMac 6100 and would like to be your beta tester. My e-mail address is "david@helium.ch.ntu.edu.tw". Thanks! Sincerely, David, Tsu-chien Weng National Taiwan Univ. From serg@markov.chem.rochester.edu Sat Feb 3 10:09:52 1996 Received: from galileo.cc.rochester.edu for serg@markov.chem.rochester.edu by www.ccl.net (8.6.10/950822.1) id KAA29407; Sat, 3 Feb 1996 10:09:21 -0500 Received: from markov.chem.rochester.edu (markov.chem.rochester.edu [128.151.176.16]) by galileo.cc.rochester.edu (8.7.1/8.6.4) with SMTP id KAA18019 for <@galileo.cc.rochester.edu:chemistry@www.ccl.net>; Sat, 3 Feb 1996 10:09:20 -0500 (EST) Received: by markov.chem.rochester.edu (920330.SGI/920502.SGI.AUTO) for @galileo.cc.rochester.edu:chemistry@www.ccl.net id AA27113; Sat, 3 Feb 96 10:09:20 -0500 Date: Sat, 3 Feb 1996 10:09:06 -0500 (EST) From: Sergei Tretiak To: chemistry@www.ccl.net Subject: Fock and other hamiltonian matrices in G94 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I'm looking how to print from G94 some hamiltonian matrices. Something I found but many questions are still opened. I will use the terminology of the famous A.Szabo & N.Ostlund 'Modern Quantum Chemistry' book. How to print: 1.Fock matrix F (Probably the easiest way is to use NBO block: $NBO keywords FAO, FNAO, .....-any basis set can be chosen) 2.Core-Hamiltonian h(1). (Can be printed by using IOP(3/33=1-5) to print one and two electron integrals) 3.An effective one-electron potential-the Hartree-Fock potential v(1). I have no idea how to get it. Presumably F=h(1)+v(1). It is possible to print two electron integrals, but how to treat and relate them to v(1)? Any information would be appreciated. Thanks in advance for your answers. Sincerely, Sergei Tretiak From owner-chemistry@ccl.net Sat Feb 3 10:39:52 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA29569; Sat, 3 Feb 1996 10:31:48 -0500 Received: from UMSLVMA.UMSL.EDU for wwelsh@jinx.umsl.edu by bedrock.ccl.net (8.7.1/950822.1) id KAA01208; Sat, 3 Feb 1996 10:31:47 -0500 (EST) Received: from admiral.umsl.edu by UMSLVMA.UMSL.EDU (IBM VM SMTP V2R2) with TCP; Sat, 03 Feb 96 09:32:54 CST Received: from [134.124.76.179] by admiral.umsl.edu (5.4R3.10) id AA18238; Sat, 3 Feb 1996 09:31:44 -0600 Message-Id: <9602031531.AA18238@admiral.umsl.edu> X-Sender: wwelsh@jinx.umsl.edu X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sat, 03 Feb 1996 09:33:48 -0600 To: chemistry@ccl.net From: wwelsh@jinx.umsl.edu (William Welsh) Subject: Force-field parameters for Ferric Ion (FE3+) Dear Netters, I am looking for any references to molecular mechanics force-field parameters for FE3+ in protein environments. I prefer Discover-type parameters, AMBER-type parameters, or Sybyl-type parameters. Thanks ... Bill Welsh Dept. of Chemistry Univ. of Missouri-St. Louis From owner-chemistry@ccl.net Sat Feb 3 13:39:54 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA00753; Sat, 3 Feb 1996 13:29:46 -0500 Received: from mha-ibm2.umd.edu for mha@mha-ibm2.umd.edu by bedrock.ccl.net (8.7.1/950822.1) id NAA02095; Sat, 3 Feb 1996 13:29:44 -0500 (EST) Received: by mha-ibm2.umd.edu (AIX 3.2/UCB 5.64/4.03) id AA15158; Sat, 3 Feb 1996 13:22:47 -0500 From: mha@mha-ibm2.umd.edu (millard alexander) Message-Id: <9602031822.AA15158@mha-ibm2.umd.edu> Subject: conference announcement To: chemistry@ccl.net Date: Sat, 3 Feb 96 13:22:46 EST X-Mailer: ELM [version 2.4dev PL17] could you please put the following link in your database of conferences of interest to computation and theoretical chemists Symposium on Bimolecular Interactions of Small Free Radicals ACS National Meeting, Division of Physical Chemistry, Orlando, FL August 25-29, 1996 organizers: M. H. Alexander (Maryland) and P. J. Dagdigian (Johns Hopkins) for more information: http://www-mha.umd.edu/~mha/acs.html -- Millard Alexander tel. (301) 405.1823; fax: 1.301.314.9121 Department of Chemistry and Biochemistry University of Maryland College Park, MD 20742-2021, USA internet: mha@mha-ibm2.umd.edu WWW: http://www-mha.umd.edu From nash@chem.wisc.edu Sat Feb 3 23:40:02 1996 Received: from audumla.students.wisc.edu for nash@chem.wisc.edu by www.ccl.net (8.6.10/950822.1) id XAA03159; Sat, 3 Feb 1996 23:29:44 -0500 Received: from [144.92.180.109] by audumla.students.wisc.edu; id WAA73886; 8.6.9W/42; Sat, 3 Feb 1996 22:29:38 -0600 X-Sender: jrnash@students.wisc.edu Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sat, 3 Feb 1996 22:29:39 -0600 To: CHEMISTRY@www.ccl.net From: nash@chem.wisc.edu (John R. Nash) Subject: SUMMARY: From one molecule to another Cc: felice@bioorganic.mechanisms.ucsb.edu, Jeffrey.Gosper@brunel.ac.UK, thomas_w@btm2x2.mat.uni-bayreuth.DE My original post: > I am seeking a utility that will take as input the cartesian >coordinates >of compounds A and B and generate x number of intermediate structures in >between the two by interpolation (i.e. morphing from one structure to the >other). I know that some packages will do this sort of thing for "linear >synchronous transit" calculations, but I need the input files for a >computation where this is not included. (The molecule is way too big for >GAUSSIAN... could the program perhaps be convinced to calculate the >coordinates w/o running the qm calculation on them?) This seems like an >simple enough utility to write, but my guess is that it must have been done >by someone... As I suspected, this is a problem tackled by many. I've collected all of the responses that have appeared on the list and in my mailbox together here. The method that I used was to use the -spline function of Babel, since I was already familiar with the program. ---------------------------------------------------------------------- From: Pat Walters Babel can do this. Matt Stahl added some code to create a spline between two structures. If you contact Matt (stahl@laura.harvard.edu) he can give you the details. Pat ------------------------------------------------------------------ W. Patrick Walters, Ph.D. Scientist, Computational Chemistry and Molecular Modeling Vertex Pharmaceuticals, Inc., 40 Allston St., Cambridge, MA 02139 Voice: (617)576-3111 FAX: (617)576-2109 ---------------------------------------------------------------------- From: Ernest Chamot MOPAC, being a semiempirical method, can handle a much larger system than a Gaussian ab initio calculation, and I thought that MOPAC would do the job for you with a "SADDLE" calculation, selecting XYZ to keep the calculation using cartesian coordinates, rather than internal coordinates. I tried it out, though, and the MOPAC Output file does indeed have the initial and final geometries in cartesian coordinates, but the intermediate steps are all in internal coordinate format! You should be able to convert each of these internal coordinate Z-matrices into a cartesian representation with an additional MOPAC run (1SCF) for each step, but I'm afraid this isn't a very elegant solution. EC --- Ernest Chamot Consultant in Computational Chemistry Applications Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 (708) 637-1559 (Voice & Fax) echamot@xnet.com ---------------------------------------------------------------------- From: Wayne Huang Seems you want to a dynamic constrain exercise. Coordinate driving which allow one to generate a list of molecule by promoting its geometrical parameters (can be more than one simultaneously or in sequence) of a single structure, but this requires optimization of some sort, at least MM. --Wayne -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92715 | | Wavefunction, Inc. | (714)955-2120 Fax: (714)955-2118 | | huang@wavefun.com | World Wide Web: http://wavefun.com | +---------------------------------------------------------------------+ ---------------------------------------------------------------------- From: W.P.vanHoorn@ct.utwente.nl (Willem Paul van Hoorn) [author included source code for two programs. here are the headers] #!/bin/ksh # # crd2mind_kollman : convert and append CHARMM .CRD file to an input for BOSS MIND # The Kollman reaction coordinate is generated: J.Chem.Phys. 97, 5108 (1992) # lamda = 0: start structure; lambda = 1: final structure # sigma/epsilon/atom symbol are not added # Usage: crd2mind in[.CRD] # by WPvH 1994 # #!/bin/csh # # crd2mind_all_kolman : appends single MIND files to one, # appends non bonded params # lambda = 0: start structure; lambda = 1: final structure # pastefile: paste -d" " lambda0.CRD lambda1.CRD > pastefile.paste # by WPvH 1994 ---------------------------------------------------------------------- Thanks to all who replied!!! -john nash -==-John R. Nash-==-nash@chem.wisc.edu-==-UW-Madison Chem. Dept-==- --- "When in doubt, roll!" ---