From chemistry-request@server.ccl.net Sun Nov 5 11:03:01 2000 Received: from dragon.inha.ac.kr (dragon.inha.ac.kr [165.246.10.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA26967 for ; Sun, 5 Nov 2000 11:02:59 -0500 Received: (from kckyung@localhost) by dragon.inha.ac.kr (8.9.1a-H1/8.9.1) id AAA18221 for chemistry@ccl.net; Mon, 6 Nov 2000 00:45:33 +0900 (KST) From: Chan Kyung Kim Message-Id: <200011051545.AAA18221@dragon.inha.ac.kr> Subject: GAMESS : DISK SPACE LIMIT To: chemistry@ccl.net Date: Mon, 6 Nov 100 00:45:32 +0900 (KST) X-Mailer: ELM [version 2.4 PL21-h4] MIME-Version: 1.0 Content-Type: text/plain; charset=EUC-KR Content-Transfer-Encoding: 8bit Dear Computational Chemists: I have a problem related to the GAMESS package running under PC Linux. My molecule is exceeding 2GB limit. I searched the CCL and found similar question but no answer was given. So, please tell me how to solve this problem (I know Gaussian can do this by splitting files). Chan. From chemistry-request@server.ccl.net Sun Nov 5 12:24:17 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA27209 for ; Sun, 5 Nov 2000 12:24:17 -0500 Received: from hotmail.com (f100.law6.hotmail.com [216.32.241.100]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id MAA00299 for ; Sun, 5 Nov 2000 12:24:02 -0500 (EST) Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sun, 5 Nov 2000 09:23:42 -0800 Received: from 213.174.2.2 by lw6fd.law6.hotmail.msn.com with HTTP; Sun, 05 Nov 2000 17:23:42 GMT X-Originating-IP: [213.174.2.2] From: "dido dido2" To: chemistry@ccl.net Subject: hello Date: Sun, 05 Nov 2000 17:23:42 GMT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 05 Nov 2000 17:23:42.0829 (UTC) FILETIME=[252F61D0:01C0474D] Can you tell me the formula for determination number of isomers according to number of carbon atoms at alkanes?? please _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. Share information about yourself, create your own public profile at http://profiles.msn.com. From chemistry-request@server.ccl.net Sun Nov 5 17:32:16 2000 Received: from interlock.herc.com (interlock.herc.com [199.221.7.2]) by server.ccl.net (8.8.7/8.8.7) with SMTP id RAA28395 for ; Sun, 5 Nov 2000 17:32:15 -0500 From: Goutam.Das@betzdearborn.com Received: from csdnsg1.herc.com ([147.116.14.51]) by interlock.herc.com with SMTP id RAA19534 (InterLock SMTP Gateway for ); Sun, 5 Nov 2000 17:32:14 -0500 Subject: wax crystals To: CHEMISTRY@ccl.net X-Mailer: Lotus Notes Release 5.0.2b December 16, 1999 Message-Id: Date: Sun, 5 Nov 2000 16:30:48 -0600 X-Priority: 3 (Normal) X-Mimetrack: Serialize by Router on CSDNSG1/Servers/Herc(Release 5.0.1b|September 30, 1999) at 11/05/2000 05:21:52 PM Mime-Version: 1.0 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 RAA28396 Dear CCLers I few weeks back I posted a question on references/websites related to n-alkane crystals. I would like to thank all of you who replied and assure you that I will be in touch with you in in the future. The responses are summarized below: (1) "I spent a number of years (5 in fact) looking at the crystallisation and structure of diesel waxes. Probably the two most relevant papers that I can think of (and coincidentally I am an author on) are A.R. Gerson, S.C. Nyburg and A. McAleer, Crystal structures and voids in diesel waxes, Journal of Applied Crystallography, 32, 296-299 (1999) A.R. Gerson, S.C. Nyburg, Structures of two binary n-alkane solid solutions, Acta. Cryst., B50, 252-256 (1994) I actually did my Ph.D. in this area so if you are interested I can photocopy the reference list out of my thesis and fax it to you - it is a bit out of date now but may be of some use. Best regards Andrea Gerson (2) Just dropping in my 2 pence worth... You will find a couple long-chain fatty acids complexes in an article we recently published: Boström, Norrby, and Liljefors, "Conformational Energy Penalties of Protein-Bound Ligands", J.Comput.-Aid.Mol.Des.,12,383,1998. However, you should be cautious when analyzing the 'bioactive' conformations. That is, the resolution of the complexes is probably not sufficient to unambiguously determine the 'bioactive' conformation. A source for protein-ligand complexes, which I find very useful, is the ReLiBase homepage: http://relibase.ebi.ac.uk/ Hope this helps. Regards Jonas ----------------------------------------------------------------- Jonas Boström, PhD Computational Chemist Department of Medicinal Chemistry AstraZeneca R&D Mölndal S-431 83 Mölndal Sweden Tel +46 31 706 52 51 Fax +46 31 776 37 10 Email jonas.bostrom@astrazeneca.com You might be interested in my web page, whose address is given below. -- 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 (3) I've been working on the crystal structures of n-alkanes for the past 4 years, so I can give you some references. A good paper to start with would be S.C. Nyburg & J.A. Potworowski, Acta Cryst. B29 (1973) pp. 347-352. It contains all relevant crystal structures of even n-alkanes except one. That one is described in R. Boistelle, B. Simon & G. Pepe, Acta Cryst B32 (1976) pp. 1240-1243. For odd n-alkanes, see A.E. Smith, J. Chem. Phys 21 (1953) pp. 2229-2231 and W. Piesczek, G.R. Strobl & K. Malzahn, Acta Cryst. B30 (1974) pp. 1278-1288. I possess all structures mentioned in electronical form, in varying degrees of completeness and in several file formats. If you're interested, e-mail me. There are also papers on phase behaviour (e.g. Turner), crystal growth (search for 'R. Boistelle'), binary and ternary mixtures (search for 'D. Mondieig') and waxes (search for 'D. L. Dorset'). If you're going to do molecular modelling, there is some additional stuff you might need to know. Just e-mail me if you have any further questions. With kindest regards, -- Jacco van de Streek, Dept. of Solid State Chemistry, University of Nijmegen, Toernooiveld 1, 6525 ED NIJMEGEN, The Netherlands. Tel.: +31 (0)24 3652831 Fax : +31 (0)24 3653067 e-mail: mailto:jaccos@sci.kun.nl Goutam Das Research Scientist BetzDearborn Division of Hercules The Woodlands, TX 77380 281.367.6201 ext 425 From chemistry-request@server.ccl.net Sun Nov 5 22:02:03 2000 Received: from sunflare.ccs.yorku.ca (sunflare.ccs.yorku.ca [130.63.236.128]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA29373 for ; Sun, 5 Nov 2000 22:02:03 -0500 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sunflare.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id WAA06966 for ; Sun, 5 Nov 2000 22:01:57 -0500 (EST) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id eA631we13630 for chemistry@ccl.net; Sun, 5 Nov 2000 22:01:58 -0500 (EST) From: Wai-To Chan Message-Id: <200011060301.eA631we13630@curl.gkcl.yorku.ca> Subject: Gaussian: recalculating thermochem To: chemistry@ccl.net Date: Sun, 5 Nov 2000 22:01:57 -0500 (EST) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit To Jeremey Greenwood, Appended to this message is a piece of FORTRAN code (thermo.f) that may serve your purpose. It can evaluate thermochemical quantities including vibrational and rotational entropies as well as total enthalpy (H) and free energy (G) at a temperature specified within the program using quantities from a gaussian 98 harmonic vibrations output file. I guess the program you already received from other would do this but this program may still help you with developing an automatic procedure. You only have to specify the name of the g98 file and the program would read off the harmonic vibrations from the file. To get the program to run follow these steps Compile and link the program f77 thermo.f I compiled the program on a SGI machine but it should run on AIX and other major unix stations. Submit a g98 harmonic vibration file done with default settings xxx.log to a test run. You should get a listing of thermal quantities which duplicates those in your g98 output file. So if you want to repeat your old g98 jobs redone at different temperature simply repeat the run with the setting of temp from 298.15 K changed to the desired value. Obviously writing such a tiny program doesn't require much imagination and everyone who finds it useful are welcomed to download it. But since I lifted the two major subroutines for parsing the g98 file >from external source please retain the comments where I acknowledged their original source in any future modifications. Wai-To Chan C****************thermal.f********************* c234567890123456789012345678901234567890123456789012345678901234567890 program read C integer ncard, nome, num, zero integer index, NUMBER, ILEN integer i,j, lpst, nflag, nrot real*8 dnum, omega(100), vthe(100), therm real*8 mass, mmass, II(4), I1, I2, I3, Rconv real*8 Ezpe, Esum, temp, Kb, R, sum, autoj real*8 hP, pie, Nav, qtran, qrot, qvib real*8 Stran, Srot, Svib, Evib, Etrn, Erot real*8 utokg, jtoc, molV, sigma, totS, totE, totG real*8 one, oneh, half, two, hc, term, totH real*8 sumvE, sumvS, theT, ext c Size of Gaussian 98 output file is set to 10000 lines character*80 line(10000) character*14 freq /'Frequencies --'/ character*15 molM /'Molecular mass:'/ character*26 rotcs /'ROTATIONAL CONSTANTS (GHZ)'/ character*25 rotc /'ROTATIONAL CONSTANT (GHZ)'/ character*26 rots /'ROTATIONAL SYMMETRY NUMBER'/ character*22 zcorr /'Zero-point correction='/ character*32 sumof /'Sum of electronic and zero-point'/ character*4 LEXT /'.log'/ character*40 RNT1 parameter(zero=0,Kb=1.381D-23,jtoc=1.D0/4.184D0) parameter(hP=6.626D-34,pie=22.D0/7.D0,Nav=6.022D23) parameter(R=8.314D0,molV=24.79D-3,utokg=1.661D-27) c parameter(R=8.314D0,molV=1.D-4,utokg=1.661D-27) c Change the value of temp set below if you c want to calculate H and G at different temperature parameter(temp=298.15D0,hc=6.626D-34 * 2.998D10) parameter(Rconv=16.86D0*1.661D-27*1.D-20,autoj=627.5D0*4.184D3) parameter(one=1.D0,oneh=1.5D0,half=0.5D0,two=2.D0) c Use .log as extension of your g98 output file as in xxx.log call MAKNAME(1,RNT1,ILEN,LEXT) if (ILEN .EQ. 0) stop 'usage: a.out file1' open (unit=11, file=RNT1, form='formatted') write(6,'(a,a/)') 'Gaussian output file: ', RNT1 30 format(a80) ncard=1 nome=1 80 continue read(11,30,end=90) line(ncard) ncard=ncard+1 goto 80 c 90 continue c ncard = ncard - 1 nrot=1 nome=1 do 100 i = 1, ncard c if (index(line(i), freq) .ne. zero) then lpst = 16 do 50 j = 1, 3 nflag = NUMBER(line(i), lpst, num, omega(nome)) if (nflag .gt. 0) goto 100 nome = nome + 1 50 continue endif c if (index(line(i), molM) .ne. zero) then lpst=17 nflag = NUMBER(line(i), lpst, num, mmass) endif if (index(line(i), zcorr) .ne. zero) then lpst=24 nflag = NUMBER(line(i), lpst, num, Ezpe) endif if (index(line(i), sumof) .ne. zero) then lpst=44 nflag = NUMBER(line(i), lpst, num, Esum) endif c if (index(line(i), rots) .ne. zero) then lpst=28 nflag = NUMBER(line(i), lpst, num, sigma) endif if (index(line(i), rotc) .ne. zero) then lpst=28 nrot=1 nflag = NUMBER(line(i), lpst, num, II(nrot)) endif if (index(line(i), rotcs) .ne. zero) then nrot=3 do 51 j = 1, 3 nflag = NUMBER(line(i), lpst, num, II(j)) 51 continue endif c 100 continue close(11) write(6,41) 'Molecular mass/amu', mmass write(6,'(a,3f12.6)') * 'Rotational Constants: ', (II(j), j = 1, nrot) write(6,41) 'Zero-point correction: ', Ezpe write(6,41) 'Sum of electronic and zero-point energies: ', Esum write(6,*) 'number of vibrations: ', nome-1 41 format(a,g12.6/) c Evaluate translational partition function qtran c234567 c qtran=dsqrt((2.*pie*mmass*Nav*Kb*temp)/(hP**2)) mass = mmass * utokg therm = hP * dsqrt(1.D0/(2.D0 * pie * mass * Kb*temp)) qtran = molV/(therm**3) Stran = 2.5D0*R + R*dlog(qtran/Nav) c Stran = 2.5D0*R + R*dlog(qtran) Etrn = oneh*R*temp write(6,*) 'Translational Q E S ' write(6,'(11x,3g12.4/)') qtran, Etrn*jtoc/1.D3, Stran*jtoc c Evaluate rotational partion function qrot qrot = 8.D0 * pie**2 * Kb * temp / hP**2 if (nrot .eq. 1) then I1 = Rconv/(.0334D0*II(1)) qrot = qrot * I1 / sigma Erot = R*temp Srot = one*R + R*dlog(qrot) else I1 = Rconv/(.0334D0*II(1)) I2 = Rconv/(.0334D0*II(2)) I3 = Rconv/(.0334D0*II(3)) qrot = dsqrt(pie) * qrot**oneh * dsqrt(I1*I2*I3) / sigma c23456789012345678901234567890123456789012345678901234567890123456789012 Erot = oneh*R*temp Srot = oneh*R + R*dlog(qrot) endif write(6,*) 'Rotational Q E S ' write(6,'(8x,3g12.4/)') qrot, Erot*jtoc/1.D3, Srot*jtoc c Evaluate vibrational partition function qvib=one sumvE = 0.D0 sumvS = 0.D0 c omega(j) contains valueso harmonic frequencies read off your g98 output file do 42 j = 1, nome-1 vthe(j) = hc*omega(j)/Kb theT = vthe(j)/temp ext = dexp(theT) sumvE = vthe(j)/two + vthe(j) * (one / (ext - 1) ) + sumvE sumvS = (theT/(ext - one) - dlog(one - (one/ext)) ) + sumvS c c if (j .eq. 1) write(6,*) 'vib1 S: ', R*sumvS/jtoc c qvib = qvib * (dexp(-vthe(j)/(two*temp)) / c 1 (1 - dexp(-vthe(j)/temp))) c term = (one/dsqrt(ext))/(one - (one/ext)) term = one/(one - one/ext) qvib = qvib*term c234567 42 continue Evib = R*sumvE Svib = R*sumvS write(6,*) 'Vibrational Q E S ' write(6,'(13x,3g12.4/)') qvib, Evib*jtoc/1.D3, Svib*jtoc totS = Stran + Srot + Svib totE = Esum + (Etrn + Erot + Evib)/autoj - Ezpe totH = totE + R*temp/autoj totG = totH - temp*totS/autoj write(6,111) 'Total partition function: ', qtran*qvib*qrot write(6,111) 'Total entropy: ', totS*jtoc write(6,111) 'Total zero-temp energy: ', Esum write(6,111) 'Thermal correction: ', (Etrn + Erot + Evib)/autoj 1 - Ezpe write(6,111) 'Total thermal energy: ', totE write(6,111) 'Total enthalpy: ', totH write(6,111) 'Total free energy: ', totG 111 format (a,g14.8) stop end c C W.-T. Chan notes: This subroutine is taken from the McMaster AIMPAC package SUBROUTINE MAKNAME(I,STRING,L,EXT) CHARACTER*(*) STRING,EXT INTEGER I,J,N,L CALL GETARG(I,STRING) J = LEN(STRING) DO 10 N = 1,J IF(STRING(N:N) .EQ. ' ') THEN L = N - 1 STRING = STRING(1:L)//EXT RETURN ENDIF 10 CONTINUE STOP ' FAILED TO MAKE A FILE NAME ' END c cWai-To Chan note: This routine is taken from the McMaster AIMPAC package. C SKK ================================================================== SKK C FUNCTION NUMBER (LINE, LPST, NUM, DEC) C C CONVERTS A CHARACTER STRING OF NUMBERS INTO ACTUAL NUMBERS EITHER C INTEGERS OR DECIMAL MAY BE READ. C NUMBER = 1 IF ALL THE REMAINING CHARACTERS ARE BLANK C = 2 IF CHARACTERS ARE NOT RECOGNISED AS A NUMBER, LPST IS RESET C SKK ================================================================== SKK DOUBLE PRECISION DEC, TEN CHARACTER*(*) LINE CHARACTER BLANK, COMMA, DOT, MINUS, L CHARACTER CTEN(0:9) DATA CTEN /'0','1','2','3','4','5','6','7','8','9'/ PARAMETER (BLANK = ' ', COMMA = ',') PARAMETER (DOT = '.', MINUS = '-') INTEGER ITEN PARAMETER (ITEN = 10, TEN = 10.0D0) NUM = 0 DEC = 0.0D0 NP = 0 ND = 0 MS = 0 NUMBER = 0 LPEND = LEN (LINE) 5 IF (LINE(LPST:LPST) .EQ. BLANK) THEN LPST = LPST + 1 IF (LPST .GT. LPEND) THEN NUMBER = 1 RETURN END IF GOTO 5 END IF LBEFOR = LPST DO 1 I = LBEFOR, LPEND LPST = I L = LINE(I:I) IF (L .EQ. BLANK .OR. L .EQ. COMMA) THEN GOTO 2 ELSE IF (L .EQ. MINUS) THEN MS = 1 GOTO 1 ELSE IF (L .EQ. DOT) THEN NP = 1 GOTO 1 END IF DO 3 J = 0, 9 IF (L .EQ. CTEN(J)) THEN N = J GOTO 4 END IF 3 CONTINUE NUMBER = 2 LPST = LBEFOR RETURN 4 IF (NP .EQ. 1) THEN ND = ND + 1 DEC = DEC + DFLOAT(N)/TEN**ND ELSE NUM = NUM*ITEN + N END IF 1 CONTINUE 2 DEC = DFLOAT(NUM) + DEC IF (MS .EQ. 0) RETURN DEC = -DEC NUM = -NUM RETURN END