From antony@indigo.ucdavis.edu Wed Nov 5 01:35:16 1997 Received: from indigo.ucdavis.edu for antony@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id BAA06241; Wed, 5 Nov 1997 01:02:47 -0500 (EST) Received: from indigo.ucdavis.edu by indigo.ucdavis.edu via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id WAA02286; Tue, 4 Nov 1997 22:04:59 -0800 Date: Tue, 4 Nov 1997 22:04:59 -0800 (PST) From: Jens Antony To: chemistry@www.ccl.net Subject: Protein DNA Docking Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everybody. As part of my project I have to dock an enzyme with a piece of DNA. Although this task can be done with standard molecular modeling programs such as InsightII, I would like to know which one of the many specialized programs for ligand-receptor docking is best suited to this task. Thanks for your interest and help. P.S. Reference to review articles is appreciated. ---- Jens Antony Department of Chemistry University of California Davis, CA 95616 antony@indigo.ucdavis.edu Tel: 916-754-8695 From chaudash@helios.aston.ac.uk Wed Nov 5 05:35:19 1997 Received: from hermes.aston.ac.uk for chaudash@helios.aston.ac.uk by www.ccl.net (8.8.3/950822.1) id EAA06914; Wed, 5 Nov 1997 04:58:00 -0500 (EST) Message-Id: <199711050958.EAA06914@www.ccl.net> Received: from mb51910.aston.ac.uk by hermes.aston.ac.uk with SMTP (PP); Wed, 5 Nov 1997 10:01:26 +0000 Comments: Authenticated sender is From: chaudash@aston.ac.uk Organization: aston.ac.uk To: chemistry@www.ccl.net Date: Wed, 5 Nov 1997 10:04:50 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: qm calculations on Al complexes. Reply-to: chaudash@aston.ac.uk X-Confirm-Reading-To: chaudash@aston.ac.uk X-pmrqc: 1 Return-receipt-to: chaudash@aston.ac.uk Priority: normal In-reply-to: <345FD8F1.5B9E@eecs.uic.edu> X-mailer: Pegasus Mail for Windows (v2.54) HELP!!!! Has anyone done any qm caculations on organo-metallic calculations involving aluminium. In particular with the PM3 basis set, but any will do. If you have I'd appreciate your advice on a few matters. Waiting eagerly in anticipation. From jcf@bureau.pharmacie.unicaen.fr Wed Nov 5 08:35:21 1997 Received: from bureau.pharmacie.unicaen.fr for jcf@bureau.pharmacie.unicaen.fr by www.ccl.net (8.8.3/950822.1) id HAA07538; Wed, 5 Nov 1997 07:56:28 -0500 (EST) Received: by bureau.pharmacie.unicaen.fr (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id NAA11795; Wed, 5 Nov 1997 13:46:27 +0100 From: "Jean-Christophe" Message-Id: <9711051346.ZM11793@bureau.pharmacie.unicaen.fr> Date: Wed, 5 Nov 1997 13:46:19 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: organic molecules and chemical functions II Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLess, Yesterday I wrote the following message >I am looking for a program to determine and to code the chemical functions >(i.e., epoxide, fused rings, amines ...) of small organic molecules (I have the >codes SMILES of these molecules). >Would any one please give me any information about where can I find programs to >do this ? > >Thanks a lot in advance. Thanks for all who answered my question, but I want to clarify it. I dont need information about codes SMILES, I need a program that determine by a macro the presence or not of chemical functions of many molecules. By exemple Molecule 1: 1 function ester, 2 fused rings, 0 function amine, ... Molecule 2: 0 function ester, 0 fused rings, 2 functions amine, ... Molecule n: 2 functions ester, 2 fused rings, 2 functions amine, ... Thanks -- ------------------------------------------ FAUCON Jean-Christophe UFR de Pharmacie Universite de Caen FRANCE email: jcf@bureau.pharmacie.unicaen.fr ------------------------------------------ From ccl@www.ccl.net Thu Oct 30 14:34:38 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id NAA23016; Thu, 30 Oct 1997 13:48:10 -0500 (EST) Received: from msuvx1.memphis.edu for tcundari@cc.memphis.edu by bedrock.ccl.net (8.8.6/950822.1) id NAA20603; Thu, 30 Oct 1997 13:47:57 -0500 (EST) Received: from [141.225.145.9] by MSUVX1.MEMPHIS.EDU (PMDF V5.1-8 #16781) with SMTP id <01IPF2MBDXQO9C2RCZ@MSUVX1.MEMPHIS.EDU> for chemistry@ccl.net; Thu, 30 Oct 1997 12:48:02 CST Date: Thu, 30 Oct 1997 12:48:39 -0600 From: tcundari@cc.memphis.edu (Tom Cundari) Subject: Re: Relativistic correction for lanthanides, try # 2 To: slawek@alchmist.scs.uiuc.edu Cc: chemistry@ccl.net Message-id: MIME-version: 1.0 Content-type: text/plain; charset="us-ascii" Dear Dr. Janicki, The easiest way to treat the relativistic effects is to use a relativistic ECP (i.e., one derived from an all-electron Dirac Hartree Fock calc). We have developed and tested an ECP scheme for the lanthanides in collab. with Walt Stevens @ NIST. In my opinion, however, the best work in this area has been done by Drs. Dolg, Preuss, Stoll and their cowrokers @ Stuttgart. Ermler et al. have recently reported a Ln ECP scheme. If you're dedicated to all-electron calcs I would suggest the following review by Pyykko. P Pyykko Chem. Rev. 1988, 88, 563. Tom Cundari Associate Professor =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+ Tom Cundari Department of Chemistry Associate Professor The University of Memphis e-mail:tcundari@cc.memphis.edu Memphis, TN 38152-6060 phone: 901-678-2629 FAX: 901-678-3447 http://www.chem.memphis.edu/umchem.html **** U of Memphis is searching for an Asst. Prof. of Computational Chemistry, contact me by email for details or see these URLs www.chem.memphis.edu/ccad.html www.chem.memphis.edu/ccletter.html **** =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+ From willsd@conrad.appstate.edu Thu Oct 30 18:34:35 1997 Received: from am.appstate.edu for willsd@conrad.appstate.edu by www.ccl.net (8.8.3/950822.1) id RAA24821; Thu, 30 Oct 1997 17:45:44 -0500 (EST) Received: from spd2.appstate.edu (SYSTEM@spd2.appstate.edu [152.10.1.27]) by am.appstate.edu (8.8.5/8.8.5) with ESMTP id RAA09391 for ; Thu, 30 Oct 1997 17:45:34 -0500 (EST) Received: from dft ("port 1103"@dft.chem.appstate.edu) by conrad.appstate.edu (PMDF V5.1-8 #26327) with SMTP id <01IPFD07Y6669ANPAA@conrad.appstate.edu> for CHEMISTRY@www.ccl.net; Thu, 30 Oct 1997 17:45:31 DST Date: Thu, 30 Oct 1997 17:45:32 -0500 From: Steve Williams Subject: GAMESS (US) on SGI O2 X-Sender: willsd@pop.appstate.edu To: CHEMISTRY@www.ccl.net Message-id: <3.0.32.19971030174532.00933b20@pop.appstate.edu> MIME-version: 1.0 X-Mailer: Windows Eudora Pro Version 3.0 (32) Content-type: text/plain; charset="us-ascii" I am getting ready to compile GAMESS on an SGI O2 (R5000 processor) running IRIX 6.3, with version 7.1 for SGI's fortran compiler. It seems to me that I may benefit from the CCL community experience on this. I imagine that there are quite a few O2 & IRIX 6.3 GAMESS users out there and I would like to benefit from your collective wisdom. Are there any patches (I've installed the SGI recommended patches for IRIX) to the compiler that I should install? Are there any known pitfalls that I can try to avoid? Any general suggestions? Thanks, Steve ***************************************** Steve Williams F F F Chemistry \ / \ / Appalachian State University Al Al Boone, NC 28608 / \ / \ USA F F F willsd@appstate.edu From ccl@www.ccl.net Mon Nov 3 09:34:57 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id JAA25273; Mon, 3 Nov 1997 09:21:33 -0500 (EST) Received: from gatekeeper.es.dupont.com for fredvc@esalp1.dnet.dupont.com by bedrock.ccl.net (8.8.6/950822.1) id JAA10669; Mon, 3 Nov 1997 09:21:21 -0500 (EST) From: Received: by gatekeeper.es.dupont.com; id JAA04456; Mon, 3 Nov 1997 09:21:22 -0500 Received: by ns1.es.dupont.com; id AA27583; Mon, 3 Nov 97 09:18:58 -0500 Message-Id: <9711031418.AA27583@ns1.es.dupont.com> Received: from esalp1.dnet; by esds01.dnet; Mon, 3 Nov 97 09:21:21 EST Date: Mon, 3 Nov 97 09:21:21 EST To: smtp%"elewars@alchemy.chem.utoronto.ca"@cdmhvx.dnet.dupont.com Cc: mail11:;@ccl.net (@dis:chem), fredvc@esalp1.dnet.dupont.com Apparently-To: chemistry@ccl.net Subject: OVERLAP INTEGRAL AND SLATER FUNNC E. Lewars writes: >> >>1997 Nov 2 >> >> SLATER OVERLAP INTEGRALS >>>From E. Lewars >>To CCL >> >> Hello, >> >> There is some info' about overlap integrals and Slater functions that I am >>finding it hard to dig out of the literature. I should state at the outset >>that _I know_: >> >>that there are programs for calculating overlap integrals >> >>that in most molecular quantum chem Gaussian functions, not Slater functions, >>are used >> >>that Mulliken et al published a long paper (J Chem Phys, 17 (1949) 1248-1267)) >>with recipes for calculating overlap integrals >> >> >>that all kinds of tricks exist for "simplifying" the calculation of overlap >>integrals >>--------- >>OK, but what I want is simply this: >> >>(1) In the molecule H-He+ (yes, protonated helium) if the H nucleus has >> Cartesians H1(x_1, y_1, z_1) and the He nucleus He2(x_2, y_2, z_2), >> where the coordinates are in Angstroms (_not_ atomic units or Bohrs) >> >> and if we write >> >> for H: phi_1 = a_1 exp{b_1[(x-x_1)^2 + (y-y_1)^2 + (z-z_1)^2]^1/2} >> and for He: phi_2 = a_2 exp{b_2[(x-x_2)^2 + (y-y_2)^2 + (z-z_2)^2]^1/2} >> >> (usually a is expressed in terms of zeta and pi, b = -zeta, and >> the variable is a radius vector r) >> QUESTION: what are a_1 and b_1, as numbers, not Greek letters? >> what are a_2,and b_2 as numbers, not Greek letters? >> (i.e a_1 = 0.5647 or whatever, etc etc (4 decimals). The a's are normalization constants dependent on the b's; the b's are STO orbital exponents within a multiplicative factor, depending on whether Angstroms or Bohrs are being used. Search out "Slater's rules" on how to generate these exponents. >> >> S_12 = the triple integral from 0--> infinity of phi_1.phi_2 dxdydz >> must = the correct overlap, if the six Cartesian coordinates are in >> Angstroms. And of course integral of S_11 = S_22 = 1. >> The "Angstroms" restriction is a conceptual one on your part. As long as we are *consistent* in units-usage, the overlap is independent of this. >>(2) If (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, 0.800), >> (0.800 Angstroms) what is S_12 (as a number, e.g 0.4273 or whatever)? >> >>(3) For (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, d), >> is there a simple function S_12 = f(d) ? (for H, He? for any two >> 1s orbitals)? Of course f will depend parametrically on the a's and b's. You are thinking in the wrong coordinate system. STO Overlap integrals are carried out in confocal elliptical coordinates; see Eyring, Walter & Kimball, (e.g., EWK), "Quantum Chemistry", page 367. This transformation makes it convenient to express STO overlaps in terms of the A & B auxiliary functions; see Mulliken's paper, and pages 388-389 of EWK. There is lore that is almost lost on the best way(s) to generate the A & B functions. You should be aware of this before proceeding to doing actual calculations. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com -------------------------------------------------------------------------------- Opinions expressed in this electronic message should ***> NOT <*** be taken to represent the official position(s) of the DuPont Company. *****> ANY OPINIONS EXPRESSED ARE THE PERSONAL VIEWS OF THE AUTHOR ONLY. <***** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>------------- >> Thanks E. Lewars >>=============== From ccl@www.ccl.net Mon Nov 3 11:34:57 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA25942; Mon, 3 Nov 1997 11:07:57 -0500 (EST) Received: from rrzs2.rz.uni-regensburg.de for herbert.homeier@chemie.uni-regensburg.de by bedrock.ccl.net (8.8.6/950822.1) id LAA15603; Mon, 3 Nov 1997 11:07:45 -0500 (EST) Received: from rchs1.chemie.uni-regensburg.de (rchs1.chemie.uni-regensburg.de [132.199.48.1]) by rrzs2.rz.uni-regensburg.de (8.8.5/8.8.5) with SMTP id RAA15979; Mon, 3 Nov 1997 17:07:34 +0100 (MET) Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA07638; Mon, 3 Nov 97 17:59:30 +0100 Date: Mon, 3 Nov 97 17:59:30 +0100 From: Herbert Homeier t4720 Message-Id: <9711031659.AA07638@rchs1.chemie.uni-regensburg.de> To: elewars@alchemy.chem.utoronto.ca Subject: Re: CCL:G:OVERLAP INTEGRAL AND SLATER FUNNC Cc: CHEMISTRY@ccl.net Reply-To: herbert.homeier@na-net.ornl.gov Hello, > Date: Sun, 2 Nov 1997 16:54:11 -0500 (EST) > From: "E. Lewars" > Message-Id: <199711022154.QAA26919@alchemy.chem.utoronto.ca> > To: chemistry@www.ccl.net > Subject: CCL:G:OVERLAP INTEGRAL AND SLATER FUNNC > > 1997 Nov 2 > > SLATER OVERLAP INTEGRALS > >From E. Lewars > To CCL > > Hello, > > There is some info' about overlap integrals and Slater functions that I am > finding it hard to dig out of the literature. I should state at the outset > that _I know_: > > that there are programs for calculating overlap integrals > > that in most molecular quantum chem Gaussian functions, not Slater > functions, > are used > > that Mulliken et al published a long paper (J Chem Phys, 17 (1949) > 1248-1267)) > with recipes for calculating overlap integrals that contains quite a few errors .... > > that all kinds of tricks exist for "simplifying" the calculation of overlap > integrals > --------- > OK, but what I want is simply this: > > (1) In the molecule H-He+ (yes, protonated helium) if the H nucleus has > Cartesians H1(x_1, y_1, z_1) and the He nucleus He2(x_2, y_2, z_2), > where the coordinates are in Angstroms (_not_ atomic units or Bohrs) > > and if we write > > for H: phi_1 = a_1 exp{b_1[(x-x_1)^2 + (y-y_1)^2 + (z-z_1)^2]^1/2} > and for He: phi_2 = a_2 exp{b_2[(x-x_2)^2 + (y-y_2)^2 + (z-z_2)^2]^1/2} The best source of information on such questions is still the "classical" paper E. Clementi and C. Roetti, At. Data & Nucl. Data Tables 14 (1974) 177 [maybe in atomic units, though 8^)] > > (usually a is expressed in terms of zeta and pi, b = -zeta, and > the variable is a radius vector r) > QUESTION: what are a_1 and b_1, as numbers, not Greek letters? > what are a_2,and b_2 as numbers, not Greek letters? > (i.e a_1 = 0.5647 or whatever, etc etc (4 decimals). > > S_12 = the triple integral from 0--> infinity of phi_1.phi_2 dxdydz > must = the correct overlap, if the six Cartesian coordinates are in > Angstroms. And of course integral of S_11 = S_22 = 1. > > (2) If (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, 0.800), > (0.800 Angstroms) what is S_12 (as a number, e.g 0.4273 or whatever)? > > (3) For (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, d), > is there a simple function S_12 = f(d) ? (for H, He? for any two > 1s orbitals)? Of course f will depend parametrically on the a's and b's. > ------------- > Thanks E. Lewars > =============== > The answer to your final question is given below, however, in somewhat different notation: alpha : -b_1 beta : -b_2 R : d my S : Overlap of exp(-alpha*r_1) and exp(-beta*r_2), ie., for a_1=a_2=1, where r_1=sqrt(x**2+y**2+z**2) and r_2=sqrt(x**2+y**2+(z-R)**2) The result of the fortran program listed below contains also the value where a_1 and a_2 are chosen so that the 1s orbitals are normalized. See the output. There is an WWW interface to this: http://www.chemie.uni-regensburg.de/~hoh05008/form-Soverlap.html For 1s functions, of course, the result for the overlap integral does only depends on a_1,a_2,b_1,b_2 and d, not on the particular geometry of the centers (only their distance d matters). As regards units: If you enter R in Angstroem, and alpha and beta in 1/Angstroem, everything should be fine in the case of the overlap integral of normalized 1s functions. You may be interested also in the following papers: @ARTICLE{HomeierSteinborn92ote, author={H. H. H. Homeier and E. O. Steinborn}, title={On the Evaluation of Overlap Integrals with Exponential--type Basis Functions}, journal="Int. J. Quantum Chem.", volume=42, pages="761--778", year="1992" } @ARTICLE{HomeierWenigerSteinborn92pft, author={H. H. H. Homeier and E. J. Weniger and E. O. Steinborn}, title={Programs for the Evaluation of Overlap Integrals with {$B$} Functions}, journal="Comput. Phys. Commun.", volume=72, pages="269--287", year="1992" } The latter describes a fortran program package S_INT for more general orbitals. The output generated by the programs given below has been checked against the output of this package. One should be careful (!), however, with the closed form expression coded in the programs below in the case that alpha and beta are not equal, but very close, and in the case that R is small but not exactly zero. The reason is that in these cases, cancelling singularities turn up. For instance, one gets a result somewhat greater than one for the normalized functions for alpha=1.000 beta=1.001 R=0.01 and this, of course is wrong (overlaps of normalized functions have to be smaller than 1. The package S_INT generates accurate output even in the case described above. Best regards Herbert Homeier ---------------- C program ------------------------- double S(alpha,beta,R) double alpha; double beta; double R; { if (R == 0) return(8*0.3141592653589793E1/pow(alpha+beta,3)); else if (alpha != beta) return(8*0.3141592653589793E1*(-4*alpha*beta+4*exp(-(alpha-beta)*R)*alpha *beta-exp(-(alpha-beta)*R)*R*beta*beta*beta+R*alpha*alpha*alpha-R*alpha*beta* beta+exp(-(alpha-beta)*R)*R*alpha*alpha*beta)*exp(-R*beta)/R/pow(alpha+beta,3)/ pow(alpha-beta,3)); else return((R*R*alpha*alpha/3+1+R*alpha)*0.3141592653589793E1*exp(-R*alpha)/( alpha*alpha*alpha)); } -------------- maple procedure S:= proc(alpha, beta, R) if R = 0 then 8*Pi/(alpha + beta)^3 elif alpha <> beta then 8*Pi*(-4*alpha*beta + 4*exp(- (alpha - beta)*R)*alpha*beta - exp(- (alpha - beta)*R)*R*beta^3 + R*alpha^3 - R*alpha*beta^2 + exp(- (alpha - beta)*R)*R*alpha^2*beta)*exp(- R*beta) /(R*(alpha + beta)^3*(alpha - beta)^3) else (1/3*R^2*alpha^2 + 1 + R*alpha)*Pi*exp(- R*alpha)/alpha^3 fi end; --------------- f77 program including driver and overlap integral for normalized orbitals doubleprecision function S(alpha,beta,R) doubleprecision alpha doubleprecision beta doubleprecision R if (R .eq. 0.D0) then S = 8.D0*0.3141592653589793D1/(alpha+beta)**3.D0 else if (alpha .ne. beta) then S = 8.D0*0.3141592653589793D1*(-4.D0*alpha*beta+4.D0*exp(-(a #lpha-beta)*R)*alpha*beta-exp(-(alpha-beta)*R)*R*beta**3+R*alpha**3 #-R*alpha*beta**2+exp(-(alpha-beta)*R)*R*alpha**2*beta)*exp(-R*beta #)/R/(alpha+beta)**3.D0/(alpha-beta)**3.D0 else S = (R**2*alpha**2/3.D0+1.D0+R*alpha)*0.3141592653589793D1*e #xp(-R*alpha)/alpha**3 endif endif return end C program mainS double precision a,b,r,S,SS,SSS external S read(*,*,ERR=99999,END=99999) a,b,r if(a.le.0.d0) goto 99999 if(b.le.0.d0) goto 99999 if(R.lt.0.d0) goto 99999 SS=S(a,b,r) SSS=SS/0.3141592653589793D1*DSQRT(a*b)**3 write(*,*) 'int(exp(-',a,'*sqrt(x**2+y**2+z**2))' write(*,*) ' *exp(-',b,'*sqrt(x**2+y**2+(z-',r,')**2))' write(*,*) ' dx dy dz ) = ' write(*,*) ' = ',SS write(*,*) write(*,*) 'int(exp(-',a,'*sqrt(x**2+y**2+z**2))' write(*,*) ' *exp(-',b,'*sqrt(x**2+y**2+(z-',r,')**2))' write(*,*) ' dx dy dz ) /Pi *(',a,'*',b,')**(3/2) = ' write(*,*) ' = ',SSS stop 99999 write(*,*) 'Input ends or errs' stop end -------------------------------------------------------------- Priv.-Doz. Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg, D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX: +49-941-943 4719/+49-941-943 2305 email: herbert.homeier@na-net.ornl.gov WWW: http://www.chemie.uni-regensburg.de/~hoh05008 From ccl@www.ccl.net Tue Nov 4 12:35:12 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA02998; Tue, 4 Nov 1997 12:32:15 -0500 (EST) Received: from nmr.utmb.edu for robert@pauli.utmb.edu by bedrock.ccl.net (8.8.6/950822.1) id MAA22127; Tue, 4 Nov 1997 12:31:57 -0500 (EST) Received: from pauli.utmb.edu by nmr.utmb.edu via SMTP (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA09687; Tue, 4 Nov 97 11:32:33 -0600 Received: (from robert@localhost) by pauli.utmb.edu (950413.SUN.8.6.12/950213.SUN.AUTOCF) id LAA02369; Tue, 4 Nov 1997 11:32:11 -0600 From: "Robert Fraczkiewicz" Message-Id: <9711041132.ZM2367@pauli.utmb.edu> Date: Tue, 4 Nov 1997 11:32:11 -0600 References: <97103115223787@fstgvs09.tu-graz.ac.at> To: , chemistry@ccl.net Subject: Re: CCL:complex NCA Dear K. Hassler, You can generate quite equivalent purely real and purely imaginary representations by rotating in the complex plane. An example will explain that. The E symmetry block in C3 has two types of characters: 1 e e* 1 e* e where e=exp(2pi/3) and p="pi"=3.14159... By adding and subtracting these two rows you will generate real characters: 2 2c 2c where c=cos(2p/3) and imaginary ones: 0 2is 2is where s=sin(2p/3). After generating symmetry coordinates you have to normalize them anyway, so you can kick out common factors (2 and 2i): 1 c c 0 s s You will obtain perfectly real symmetry coordinates forming two separate E symmetry blocks. Since they are degenerate and give the same frequencies, you can get rid of one of them. Program RAMVIB will let you shuffle and combine symmetry blocks and isotopomers in any fashion and order. It is available from CCL archives: ftp://www.ccl.net/pub/chemistry/software/SGI/ramvib/ Happy normal-coordinate-analyzing! Robert Fraczkiewicz University of Texas Medical Branch Galveston, TX 77555, USA From taisung@chem.duke.edu Tue Nov 4 21:52:35 1997 Received: from chem.duke.edu for taisung@chem.duke.edu by www.ccl.net (8.8.3/950822.1) id VAA05448; Tue, 4 Nov 1997 21:08:37 -0500 (EST) Received: from landau.chem.duke.edu (landau.chem.duke.edu [152.3.169.83]) by chem.duke.edu (8.7.4/Duke-1.1) with ESMTP id VAA29117; Tue, 4 Nov 1997 21:08:30 -0500 (EST) Received: (taisung@localhost) by landau.chem.duke.edu (8.7.4/Duke-1.1) id VAA03636; Tue, 4 Nov 1997 21:08:29 -0500 (EST) Date: Tue, 4 Nov 1997 21:08:28 -0500 (EST) From: Taisung Lee X-Sender: taisung@landau To: Laurence Lavelle cc: chemistry@www.ccl.net Subject: Re: CCL:INCREASING CPU UTILIZATION WITH NT4 In-Reply-To: <3.0.32.19971102192050.00a1b3d0@mbi.ucla.edu> Message-ID: Hi, It seems that the computational software (HyperChem) you are using is not parallelized/multithread. NT 4.0 can accept a multithread program but it can not do multithread for a singlethread process. That means if you have a singlethread program then the maximum CPU time you can use for this program is 50% in a dual CPU machine. You can run two copies of same programs then you will get 100%. The other solution is to find a multithread computational program--I believe it is hard, because that means a parallelized program. The reason you see 54%, not 50% is that another CPU is doing other work for you.--You still get some benefit from dual-CPU :) Taisung > HI, > > > I HAVE A DUAL PENTIUM 133MHZ WITH NT4 WORKSTATION RUNNING VERY CPU > INTENSIVE CALCULATIONS (AB INITIO IN HYPERCHEM 5.02) FROM DAYS TO WEEKS > IN DURATION. > > 196 MB RAM > > 5GB VIRTUAL MEMORY (ALL SCSI HD'S WITH A SUSTAINED DATA TRANSFER RATE OF > 10MB/S.) > > (The machine could be upgraded to dual 200MMX.) > > HOWEVER TASK MANAGER SHOWS CPU UTILIZATION AT A CONSTANT 54%. > > ONLY WHEN I USE OTHER ADDITIONAL SOFTWARE DOES THE CPU UTILIZATION GO > ABOVE 54% AND UP TO 100%. > > > HOW DO I OBTAIN HIGHER (100% ?) CPU UTILIZATION WITH ONLY THE > COMPUTATIONAL SOFTWARE RUNNING? > > > > THANKS IN ADVANCED. > > > Laurence Lavelle, Ph.D. > University of California Los Angeles > Molecular Biology Institute, and Department of Chemistry & Biochemistry > Laboratory of Structural Biology & Molecular Medicine > Los Angeles, CA 90095-1570, USA > Email:LAVELLE@MBI.UCLA.EDU > Phone (Lab): (310) 206-8270 > Phone (Office): (310) 825-2083 > Fax: (310) 267-1957 > http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html From mattacf@mcmail.CIS.McMaster.CA Wed Nov 5 10:35:22 1997 Received: from mcmail.CIS.McMaster.CA for mattacf@mcmail.CIS.McMaster.CA by www.ccl.net (8.8.3/950822.1) id JAA08330; Wed, 5 Nov 1997 09:49:19 -0500 (EST) Received: from localhost (mattacf@localhost) by mcmail.CIS.McMaster.CA (8.8.5/8.8.5) with SMTP id JAA21794 for ; Wed, 5 Nov 1997 09:49:09 -0500 (EST) Date: Wed, 5 Nov 1997 09:49:09 -0500 (EST) From: "C.F. Matta" To: chemistry@www.ccl.net Subject: Hypechem Hardware Resources Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody, I am planning to upgrade a machine with the intension to purchase Hyperchem 05. I am interested to obtain highly accurate ab initio wavefunctions medium-sized organic molecules (C,O,N,H) at a RHF 6-311++G**//6-31+G* level of theory). Such molecules would have approx 70 atoms (including H), and using 6311++G** we are talking perhaps of 650 basis functions and perhaps some 1200 primitives. What sort of CPU, RAM, virtual memory, and HD space should I aim at if I'd like such a job to converge within a few days? Thank you very much. C.Matta McMaster University, Hamilton, Ontario, Canada. From boyd@chem.iupui.edu Wed Nov 5 10:39:20 1997 Received: from indyvax.iupui.edu for boyd@chem.iupui.edu by www.ccl.net (8.8.3/950822.1) id JAA08356; Wed, 5 Nov 1997 09:54:37 -0500 (EST) Received: from macgw.chem.iupui.edu by INDYVAX.IUPUI.EDU (PMDF V5.0-5 #5862) id <01IPNA6OOHW0007R92@INDYVAX.IUPUI.EDU> for chemistry@www.ccl.net; Wed, 05 Nov 1997 09:50:46 -0500 Date: Wed, 05 Nov 1997 09:52:01 -0500 From: Boyd Subject: REVIEWS IN COMPUTATIONAL CHEMISTRY To: OSC CCL Message-id: X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.0.0 Content-transfer-encoding: 7BIT CCLers, Volume 11 of REVIEWS IN COMPUTATIONAL CHEMISTRY has been published. This volume focuses on computer-aided ligand design and modeling of biomolecules. A stellar group of international scientists provide tutorials for beginners and reviews for experts. Subjects covered are: o de novo design methodologies for discovering new pharmaceuticals. o three-dimensional quantitative structure-activity relationships (3D-QSAR). o computing the lipophilic/hydrophilic behavior of molecules. o simulating DNA in the presence of counterions. o software and Internet tools for computational chemistry. The authors are: Pascal Auffinger, David L. Beveridge, Donald B. Boyd, Pierre-Alain Carrupt, David E. Clark, Patrick Gaillard, Giovanni Greco, Bhyravabhotla Jayaram, David R. Langley, Jin Li, Yvonne Connolly Martin, Mark A. Murcko, Christopher W. Murray, Ettore Novellino, Tudor I. Oprea, Ganesan Ravishanker, Bernard Testa, Chris L. Waller, and Matthew A. Young. Quoting from a review in the Journal of Medicinal Chemistry: "This well-respected series continues the fine selection of topics and presentation qualities.... For example, each chapter contains thorough treatment of the theory behind the topic being covered. Moreover, the background material is followed by ample timely examples culled from recent literature ...." The ISBN of Volume 11 is 0-471-19248-1. For more information and online indexes, visit http://chem.iupui.edu/rcc/rcc.html Thanks, Don Kenny B. Lipkowitz and Donald B. Boyd, Editors REVIEWS IN COMPUTATIONAL CHEMISTRY Department of Chemistry Indiana University-Purdue University at Indianapolis Indianapolis, Indiana 46202-3274, U.S.A. Internet boyd@chem.iupui.edu From carole@theor.ch.cam.ac.uk Wed Nov 5 11:35:22 1997 Received: from mauve.csi.cam.ac.uk for carole@theor.ch.cam.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA09175; Wed, 5 Nov 1997 10:57:19 -0500 (EST) Received: from ket.ch.cam.ac.uk [131.111.116.74] by mauve.csi.cam.ac.uk with smtp (Exim 1.73 #1) id 0xT7o2-0007Si-00; Wed, 5 Nov 1997 15:55:46 +0000 Received: (from carole@localhost) by theor.ch.cam.ac.uk (950413.SGI.8.6.12/950213.SGI.AUTOCF) id QAA05543 for CHEMISTRY@www.ccl.net; Wed, 5 Nov 1997 16:04:47 GMT From: carole@theor.ch.cam.ac.uk (Carole Van Caillie) Message-Id: <199711051604.QAA05543@theor.ch.cam.ac.uk> Subject: CCL: STANDARD LASER EXCITATION FREQUENCY ? To: CHEMISTRY@www.ccl.net Date: Wed, 5 Nov 1997 16:04:47 +0000 (GMT) X-Mailer: ELM [version 2.4 PL24 ME5a] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I would like to know if there is a standard laser excitation frequency for the experimental calculation of RAMAN Intensities/Scattering Activities. Thank you for helping me. Carole From mary@lexa.ru Wed Nov 5 15:25:15 1997 Received: from fido.transit.ru for mary@lexa.ru by www.ccl.net (8.8.3/950822.1) id OAA00453; Wed, 5 Nov 1997 14:32:41 -0500 (EST) Received: from ganzer.UUCP by fido.transit.ru with UUCP id UAA22858; (8.7.4/vak/1.9) Wed, 5 Nov 1997 20:29:59 +0300 (MSK) Received: by lexa.ru (1.65/waf) via UUCP; Wed, 05 Nov 97 20:10:10 MSK for chemistry@www.ccl.net Received: by lexa.ru (FIDO2UU 1.92e [DOS]); Wed, 5 Nov 1997 20:10:10 +0300 To: chemistry@www.ccl.net From: Marina Molchanova Message-Id: <3460A872@lexa.ru> Subject: SMOG program Date: Wed, 5 Nov 1997 20:10:10 +0300 the version of the SMOG program at ftp://ccl.ocs.edu/pub/chemistry/software/MS-DOS/SMOG has been recently updated. Thank you for your attention. Best regards, Marina Molchanova --- GoldED 2.41 From borghet@ipruniv.cce.unipr.it Wed Nov 5 16:04:05 1997 Received: from ipruniv.cce.unipr.it for borghet@ipruniv.cce.unipr.it by www.ccl.net (8.8.3/950822.1) id OAA00489; Wed, 5 Nov 1997 14:39:13 -0500 (EST) From: Received: by ipruniv.cce.unipr.it (AIX 3.2/UCB 5.64/4.03) id AA21996; Wed, 5 Nov 1997 20:04:44 +0100 Date: Wed, 5 Nov 1997 20:04:44 +0100 (NFT) Subject: PMD users To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I'm writing to know if someone use the molecular dynamics software called PMD from Columbia University to exchange information, suggestion and tricks about it. Thanking in advance for what you can do about it Best whishes Antonello Romani //\\______________________________ \\// Antonello Romani Istituto di Patologia Generale Plesso Biotecnologico Integrato Facolta' di Medicina e Chirurgia Universita' degli Studi di Parma via Volturno,39 43100 - Parma E-Mail : A.Romani@leonardo.biomed.unipr.it __________________________________//\\ \\// From Bernard.B.Pirard@GBJHA.zeneca.com Wed Nov 5 16:14:15 1997 Received: from bath.mail.pipex.net for Bernard.B.Pirard@GBJHA.zeneca.com by www.ccl.net (8.8.3/950822.1) id OAA00477; Wed, 5 Nov 1997 14:36:14 -0500 (EST) X400-Received: by mta bath.mail.pipex.net in /PRMD=pipex/ADMD=pipex/C=gb/; Relayed; Wed, 5 Nov 1997 18:07:11 +0000 X400-Received: by /PRMD=ZENECA/ADMD=PIPEX/C=GB/; Relayed; Wed, 5 Nov 1997 14:38:38 +0000 Date: Wed, 5 Nov 1997 14:38:38 +0000 X400-Originator: Bernard.B.Pirard@GBJHA.zeneca.com X400-Recipients: chemistry@www.ccl.net X400-MTS-Identifier: [/PRMD=ZENECA/ADMD=TMAILUK/C=GB/;971105143838] X400-Content-Type: P2-1984 (2) Content-Identifier: CSI NC V3.0 From: Pirard Bernard B Message-ID: <001CCC1B.MAI*/I=B/G=Bernard/S=Pirard/OU=GBJHA/PRMD=ZENECA/ADMD=PIPEX/C=GB/@MHS> To: cclq Subject: 3D profiles for protein models MIME-version: 1.0 Content-type: multipart/mixed; boundary="AkaHa2RSYQsBDiwkBHaBGN9TIxKcdXRs" --AkaHa2RSYQsBDiwkBHaBGN9TIxKcdXRs Content-type: text/plain; charset="us-ascii" [[ CCL2.TXT : 3670 in CCL2.TXT ]] --AkaHa2RSYQsBDiwkBHaBGN9TIxKcdXRs Content-type: text/plain; charset="us-ascii" Dear colleagues, I am currently looking for a WEB site with a link to a software that computes 3D profiles for a protein. I will post a summary of the replies. Thanks in advance, Bernard Pirard, PhD Computational Chemistry Group ZENECA AGROCHEMICALS Jealott's Hill Research Station Bracknell Berks RG42 6EY UK --AkaHa2RSYQsBDiwkBHaBGN9TIxKcdXRs-- From borghet@ipruniv.cce.unipr.it Wed Nov 5 16:23:46 1997 Received: from ipruniv.cce.unipr.it for borghet@ipruniv.cce.unipr.it by www.ccl.net (8.8.3/950822.1) id OAA00493; Wed, 5 Nov 1997 14:39:39 -0500 (EST) From: Received: by ipruniv.cce.unipr.it (AIX 3.2/UCB 5.64/4.03) id AA17930; Wed, 5 Nov 1997 20:10:15 +0100 Date: Wed, 5 Nov 1997 20:10:14 +0100 (NFT) Subject: Retro synthesis software To: chemistry@www.ccl.net In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Dear netters, > > I'm writing to know if someone could give me some information about some > retro synthesis software (free for academic institution could be better) > > > > Thanking in advance for what you can do about it > > Best whishes > > Antonello Romani > > > > //\\______________________________ > \\// > > > Antonello Romani > Istituto di Patologia Generale > Plesso Biotecnologico Integrato > Facolta' di Medicina e Chirurgia > Universita' degli Studi di Parma > via Volturno,39 > 43100 - Parma > > E-Mail : A.Romani@leonardo.biomed.unipr.it > > __________________________________//\\ > \\// > > > From nbaker@chemcca10.ucsd.edu Wed Nov 5 17:25:15 1997 Received: from mailbox2.ucsd.edu for nbaker@chemcca10.ucsd.edu by www.ccl.net (8.8.3/950822.1) id QAA01292; Wed, 5 Nov 1997 16:50:45 -0500 (EST) Received: from chemcca10.ucsd.edu (chemcca10.ucsd.edu [132.239.68.250]) by mailbox2.ucsd.edu (8.8.5/8.6.9) with SMTP id NAA13562 for <@ucsd.ucsd.edu:chemistry@www.ccl.net>; Wed, 5 Nov 1997 13:50:40 -0800 (PST) Received: by chemcca10.ucsd.edu (951211.SGI.8.6.12.PATCH1502/931108.SGI.ANONFTP) id NAA15682; Wed, 5 Nov 1997 13:50:40 -0800 Date: Wed, 5 Nov 1997 13:50:39 -0800 (PST) From: "Nathan A. Baker" To: CCL Subject: SUMMARY: Win95 Renderers Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A while ago I posted asking about molecule rendering programs for Win95. Here's a summary of the replies I received -- Thanks for all the help! > >I was wondering if anyone knew of any programs >(besides RasMol) for rendering molecules with >large numbers (~10000) of atoms for Windows 95 >or NT. Thanks in advance! > SwissPDB: http://expasy.hcuge.ch/spdbv/mainpage.html gOpenMol: http://laaksonen.csc.fi/gopenmol/ misc.: http://ellington.pharm.arizona.edu/~bear HyperChem 5: http://www.hyper.com MOLMOL: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ WebLab: http://www.msi.com Sculpt: http://www.intsim.com. POV-Ray: http://www.povray.org molden: ftp://ftp.caos.kun.nl/pub/molgraph/molden/bin/molden_windows_nt.zip (You need an Xwindows emulater on your windows NT machine to run it.) Alchemy 2000: http://www.tripos.com/ Chem3D: CambridgeSoft Corp. Thanks again for all your help! ---------------------------------------- Nathan Baker * nbaker@chemcca10.ucsd.edu Department of Chemistry and Biochemistry University of California, San Diego McCammon Research Group Ph:619/534-2798 ---------------------------------------- From yliu@mail.wesleyan.edu Wed Nov 5 17:37:22 1997 Received: from mail.wesleyan.edu for yliu@mail.wesleyan.edu by www.ccl.net (8.8.3/950822.1) id RAA01397; Wed, 5 Nov 1997 17:04:25 -0500 (EST) Received: from localhost (yliu@localhost) by mail.wesleyan.edu (8.8.6/8.7.3) with SMTP id RAA24939; Wed, 5 Nov 1997 17:03:40 -0500 (EST) Date: Wed, 5 Nov 1997 17:03:39 -0500 (EST) From: Yongxing Liu To: Pirard Bernard B cc: cclq Subject: Re: CCL:3D profiles for protein models In-Reply-To: <001CCC1B.MAI*/I=B/G=Bernard/S=Pirard/OU=GBJHA/PRMD=ZENECA/ADMD=PIPEX/C=GB/@MHS> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Take a look at http://www.doe-mbi.ucla.edu/Services/Verify3D.html Yongxing Liu Department of Chemistry Wesleyan University Tel: 860-343-7330 On Wed, 5 Nov 1997, Pirard Bernard B wrote: > --AkaHa2RSYQsBDiwkBHaBGN9TIxKcdXRs > Content-type: text/plain; charset="us-ascii" > > > [[ CCL2.TXT : 3670 in CCL2.TXT ]] > > --AkaHa2RSYQsBDiwkBHaBGN9TIxKcdXRs > Content-type: text/plain; charset="us-ascii" > > Dear colleagues, > I am currently looking for a WEB site with a link to a software > that computes 3D profiles for a protein. I will post a summary of > the replies. > Thanks in advance, > > Bernard Pirard, PhD > Computational Chemistry Group > ZENECA AGROCHEMICALS > Jealott's Hill Research Station > Bracknell Berks RG42 6EY > UK > > > --AkaHa2RSYQsBDiwkBHaBGN9TIxKcdXRs-- > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: Bernard.B.Pirard@GBJHA.zeneca.com > -- Original Sender From: Address: Bernard.B.Pirard@GBJHA.zeneca.com > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From kjh@cheiljedang.com Wed Nov 5 22:25:16 1997 Received: from ns.cheiljedang.co.kr for kjh@cheiljedang.com by www.ccl.net (8.8.3/950822.1) id WAA03091; Wed, 5 Nov 1997 22:05:42 -0500 (EST) Received: from reddog ([52.27.1.188]) by ns.cheiljedang.co.kr (8.6.12H1/8.6.12) with SMTP id MAA28154 for ; Thu, 6 Nov 1997 12:12:20 +0900 Sender: jhkim@ns.cheiljedang.co.kr Message-ID: <346213E6.41C6@cheiljedang.com> Date: Thu, 06 Nov 1997 11:00:54 -0800 From: Jonghoon Kim X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP20) MIME-Version: 1.0 To: CCL Subject: solubility Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers I'd like to find the package that calculate the solubility of the compound. Do you have any information? Cheers.... -- Jonghoon Kim CheilJedang corp. e-mail: kjh@cheiljedang.com