From SAVARY@sc2a.unige.ch Wed Mar 30 03:02:07 1994 Received: from chx400.switch.ch for SAVARY@sc2a.unige.ch by www.ccl.net (8.6.4/930601.1506) id CAA24835; Wed, 30 Mar 1994 02:40:47 -0500 From: X400-Received: by mta chx400.switch.ch in /PRMD=switch/ADMD=arcom/C=CH/; Relayed; Wed, 30 Mar 1994 09:40:18 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Wed, 30 Mar 1994 09:40:00 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Wed, 30 Mar 1994 11:39:37 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Wed, 30 Mar 1994 11:39:18 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Wed, 30 Mar 1994 11:39:18 +0200 Date: Wed, 30 Mar 1994 11:39:18 +0200 X400-Originator: SAVARY@sc2a.unige.ch X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=SWITCH/ADMD=ARCOM/C=CH/;<01HAKTU4Q0WS0019MZ@sc2a.unige.c] X400-Content-Type: P2-1984 (2) Content-Identifier: Symmetry the ... Alternate-Recipient: Allowed Message-ID: <01HAKTU4Q0WS0019MZ@sc2a.unige.ch> To: CHEMISTRY@ccl.net Subject: Symmetry the summary X-Envelope-to: CHEMISTRY@ccl.net X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear netters, As a friend pointed to me a forgot to summarize to the list the answers I got from my request which was the following : Dear CClers Is there an easy way (even complicated will do) to find the principal axes of symmetry of a given molecule knowing only the atoms coordinates, it is not only to be able to build internal coordinates (as MOPAC or other packages do) but to be of general use, (I think Spartan does it). Sorry if it is a FAQ. -------------------------------------------------------------- Francois Savary Department of Physical Chemistry University of Geneva 30, quai Ernest-Ansermet CH-1211 Geneva 4 phone : +4122 702 65 32 fax : +4122 702 65 18 e-mail : savary@sc2a.unige.ch -------------------------------------------------------------- Here are the answers, thanx for your precious help : ===================================================================== From: IN%"fredvc@esvax.dnet.dupont.com" 14-FEB-1994 18:57:01.28 Try the appende code to see if it does what you want. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 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. <***** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ PROGRAM MOMENTS C&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& C VERSION 3: FOR .XYZ FILES, NOT .CON FILES C************************************************************************* IMPLICIT REAL*8 (A-H,O-Z) C PARAMETER (NQ=253) PARAMETER (NMAX = NQ - 3) C LOGICAL BOHR C CHARACTER IDENT*80, DCLCMD*80, INNAME*30, NEWFIL*40, SP*2 C DIMENSION XIQ(3), QCOM(3), A(3,3), B(3), XMOM(3), V(3,3), SQ(3) DIMENSION IZ(NQ), Q(3,NQ), JCON(NQ), JATTCH(NQ,9), W(NQ), & QS(3,NQ) C REAL*8 MHZ(3) C CHARACTER*4 AXIS(3) DATA AXIS / 'I(x)', 'I(y)', 'I(z)'/ CHARACTER*1 CONS(3) DATA CONS/ 'A', 'B', 'C'/ COMMON/PASS/QV(3,3) C DIMENSION ATWT(86) COMMON/ATMDAT/AN, ATWT C DATA CAU /0.5291771E+00/ DATA HP, KHP, C0, KC0 /6.6254, -27, 2.997928, 10/ DATA SP/', '/ C PI = 4.D0 * DATAN(1.0D+00) HZF = HP/(8. * PI * PI) KHZF = KHP C&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& C GET INTIAL COORDINATES C*********************************************************************** C-----GET FILE NAME 1 WRITE(6,9999) 9999 FORMAT(/'$INPUT STRUCTURE NAME (CTRL/Z TO QUIT): ') READ(5,'(A)',END=1000)INNAME LL = INDEX(INNAME, ' ') - 1 NEWFIL = INNAME(1:LL)//'.XYZ' OPEN(UNIT=15,NAME=NEWFIL,TYPE='OLD',READONLY) C-----HOUSEKEEPING DO 2 I = 1,NQ DO 2 J = 1, 3 Q(J,I) = 0. SQ(J) = 0. 2 CONTINUE C-----READ IN DATA FOR WORKING STRUCTURE READ(15,'(A)')IDENT READ(15,*)N, ICHG, MULT, IANG IF (N.GT.NMAX) THEN WRITE(6,6999)N,NMAX STOP END IF 6999 FORMAT('0',I3,' ATOMS IS TOO MANY. LIMIT IS ',I3) NP = N + 3 BOHR = (IANG .EQ. 0) DO 5 K = 1, N READ ( 15, * ) IZ(K), (Q(I,K), I = 1, 3), NUM, JCON(K), & (JATTCH(K,L), L = 1, JCON(K)) IF (IZ(K) .LE. 86) THEN W(K)=ATWT(IZ(K)) ELSE WRITE(6,9998) K, IZ(K) CLOSE(UNIT=15) STOP END IF IF (BOHR) THEN DO 4 J = 1, 3 Q(J,K) = Q(J,K) * CAU 4 CONTINUE END IF 5 CONTINUE 9998 FORMAT(//'NO ATOMIC MASS FOR ATOM' ,I3,', ATOMIC # = ',I3) C CLOSE(UNIT=15) C*********************************************************************** C CENTER OF MASS XFORMATION C*********************************************************************** C C-----FORM MASS-WEIGHTED SUMS C DO 10 I = 1, N SW=SW+W(I) DO 9 J = 1, 3 SQ(J)=SQ(J)+W(I)*Q(J,I) 9 CONTINUE 10 CONTINUE C C-----XFORM ORIGIN TO COM DO 11 K = 1, 3 QCOM(K) = SQ(K)/SW 11 CONTINUE DO 15 L = 1, N DO 14 K = 1, 3 Q(K,L) = Q(K,L) - QCOM(K) 14 CONTINUE 15 CONTINUE C C-----ADD UNIT VECTORS TO COORDINATES DO 16 J = 1, 3 Q(J,N+J) = 1. 16 CONTINUE C*********************************************************************** C CALC. MOMENTS OF INERTIA C*********************************************************************** DO 20 I = 1, 3 DO 20 J = 1, 3 A(I,J)=0. 20 CONTINUE C C-----FORM MOMENTS MATRIX DO 25 K = 1, N A(1,1)=A(1,1)+W(K)*(Q(2,K)**2+Q(3,K)**2) A(1,2)=A(1,2)-W(K)*Q(1,K)*Q(2,K) A(2,2)=A(2,2)+W(K)*(Q(1,K)**2+Q(3,K)**2) A(1,3)=A(1,3)-W(K)*Q(1,K)*Q(3,K) A(2,3)=A(2,3)-W(K)*Q(2,K)*Q(3,K) A(3,3)=A(3,3)+W(K)*(Q(1,K)**2+Q(2,K)**2) 25 CONTINUE A(2,1) = A(1,2) A(3,1) = A(1,3) A(3,2) = A(2,3) C C-----DIAGONALIZE MOMENTS MATRIX [IMSL V1.0 ROUTINE] CALL DE2CSF(3,A,3,XMOM,V,3,B) PI = DE2ISF(3,3,A,3,XMOM,V,3,B) WRITE(6,1111) PI 1111 FORMAT('0***** DIAGONALIZATION PERFORMANCE INDEX: ',F7.3,' *****') C C-----NORMALIZE EIGENVECTORS (2-NORM) DO 29 I = 1,3 S = 0. DO 27 J = 1, 3 S = S + V(J,I)**2 27 CONTINUE S = DSQRT(S) DO 28 J = 1, 3 V(J,I) = V(J,I)/S 28 CONTINUE 29 CONTINUE C C-----TRANSFORM COORDINATES DO 34 I = 1, NP DO 33 J = 1, 3 C QS(J,I)=V(1,J)*Q(1,I)+V(2,J)*Q(2,I)+V(3,J)*Q(3,I) SUM = 0. DO 32 K = 1, 3 SUM = SUM + V(K,J)*Q(K,I) 32 CONTINUE QS(J,I) = SUM 33 CONTINUE 34 CONTINUE C C-----SCALE MOMENTS TO CGS SYSTEM KXIQ = -39 KMHZ = KHP - KXIQ - 6 DO 35 K = 1, 3 XIQ(K)=XMOM(K)/AN MHZ(K) = (HZF/XIQ(K)) * (10.**KMHZ) 35 CONTINUE C*********************************************************************** C C>>>>>CHECK FOR ENANTIOMERIZATION C*********************************************************************** DO 150 I = 1, 3 DO 150 J = 1,3 QV(J,I) = QS(J,I+N) 150 CONTINUE C CALL ORIENT C CHECK = QV(2,2) WRITE(6,5999) CHECK 5999 FORMAT('0 ENANTIOMERIC CHECK = ',F10.5) IF (CHECK.LT.0.0) THEN WRITE(6,5998) 5998 FORMAT(' ENANTIOMER OF STARTING STRUCTURE. DOING A REFLECTION' & /' THROUGH THE X-Z PLANE......'/) C DO 38 I = 1, N QS(2,I) = -QS(2,I) 38 CONTINUE END IF C C*********************************************************************** C C>>>>>DO SCREEN DUMP C*********************************************************************** C XMX=QS(1,1) XMN=XMX YMX=QS(2,1) YMN=YMX ZMX=QS(3,1) ZMN=ZMX C DO 40 I = 2, N XMX=DMAX1(XMX,QS(1,I)) XMN=DMIN1(XMN,QS(1,I)) YMX=DMAX1(YMX,QS(2,I)) YMN=DMIN1(YMN,QS(2,I)) ZMX=DMAX1(ZMX,QS(3,I)) ZMN=DMIN1(ZMN,QS(3,I)) 40 CONTINUE C C*********************************************************************** C WRITE XFORMED COORDINATES IN .XYZ_COM FILE C*********************************************************************** NEWFIL = INNAME(1:LL)//'.XYZ_COM' OPEN(UNIT=16,NAME=NEWFIL,TYPE='NEW',CARRIAGECONTROL='LIST') NEWFIL = INNAME(1:LL)//'.ROTCONS' OPEN(UNIT=6,NAME=NEWFIL,TYPE='NEW') DCLCMD = '$ TYPE/PAGE '//NEWFIL C C-----WRITE NEW .XYZ FILE IN CENTER-OF-MASS COORDINATES IF (BOHR) THEN DO 600 I = 1, N DO 590 L = 1, 3 QS(L,I) = QS(L,I)/CAU 590 CONTINUE 600 CONTINUE END IF C WRITE ( 16, 9160 ) IDENT 9160 FORMAT(A80) WRITE ( 16, 9170 ) N,SP,ICHG,SP,MULT,SP,IANG 9170 FORMAT(I3,A2,I2,A2,I1,A2,I1) IF (JCON(I) .NE. 0) THEN DO 945 I = 1, N WRITE(16,9180)IZ(I),SP,((QS(J,I),SP),J=1,3),I,SP, & JCON(I),SP,((JATTCH(I,K),SP),K=1,JCON(I)) 9180 FORMAT(I3,A2,3(F15.10,A2),I3,A2,I1,A2,9(I3,A2)) 945 CONTINUE ELSE DO 950 I = 1, N WRITE(16,9185) IZ(I),SP,((QS(J,I),SP),J=1,3),I,SP 9185 FORMAT(I3,A2,3(F15.10,A2),I3,A2,I1,A2) 950 CONTINUE END IF C WRITE(6,7999) WRITE(16,7999) 7999 FORMAT(/6X,'<-- (MOMENTS OF INERTIA) * 1.0E+39 [gm*(cm**2)]' & /6X,'(ROTATIONAL CONSTANTS) [MHz] -->'/) c DO 39 I = 1, 3 WRITE(6,7990) AXIS(I), XIQ(I), CONS(I), MHZ(I) WRITE(16,7990) AXIS(I), XIQ(I), CONS(I), MHZ(I) 39 CONTINUE 7990 FORMAT(1X,A4,' = ',G20.10,5X,A1,' = ',G20.10) C WRITE(6,4999) SW WRITE(16,4999) SW 4999 FORMAT(//5X,'PARTICLE MASS IN A.M.U = ',F15.5) C WRITE(6,7997) WRITE(16,7997) 7997 FORMAT(/13X,'MAXIMUM'7X,'MINIMUM') C WRITE(6,7996)XMX,XMN,YMX,YMN,ZMX,ZMN WRITE(16,7996)XMX,XMN,YMX,YMN,ZMX,ZMN 7996 FORMAT(3X,'X:',2F15.5/3X,'Y:',2F15.5/3X,'Z:',2F15.5) C CLOSE(UNIT=16) CLOSE(UNIT=6) C C.....TYPE SUMMARY FILE WRITE(6,1999) DCLCMD 1999 FORMAT(' ',A80) ISTAT = LIB$SPAWN(DCLCMD) IF (.NOT.ISTAT) CALL LIB$STOP(%VAL(ISTAT)) C*********************************************************************** GO TO 1 C 1000 STOP END C SUBROUTINE ORIENT C************************************************************************* IMPLICIT REAL*8 (A-H,O-Z) DIMENSION A(3,3), TMP(3) C COMMON/PASS/Q(3,3) C C C QV - CARTESIAN COORDINATES STORED COLUMN WISE C A - A TRANSFORMATION MATRIX C TMP - A TEMPORARY ARRAY C EPS - A LOWER BOUNDS FOR COMPUTATION C DATA EPS/1.0E-06/ C C************************************************************************* C C ROTATE VECTOR 3 INTO XZ PLANE [(X3,Y3,Z3) -> (X3',0,Y3)] C ASSIGN 10 TO IZERO GO TO 500 C 10 CONTINUE R = DSQRT(Q(1,3)**2 + Q(2,3)**2) IF (R.LT.EPS) GO TO 19 CT = Q(1,3)/R ST = Q(2,3)/R A(1,1) = CT A(2,2) = CT A(1,2) = ST A(2,1) = -ST A(3,3) = 1. C ASSIGN 19 TO IXFORM GO TO 600 C C************************************************************************* C C ROTATE VECTOR 3 INTO Z AXIS [(X3',0,Z3) -> (0,0,Z3)] C 19 ASSIGN 20 TO IZERO GO TO 500 C 20 CONTINUE R = DSQRT(Q(1,3)**2 + Q(3,3)**2) IF (R.LT.EPS) GO TO 29 CT = Q(3,3)/R ST = Q(1,3)/R A(1,1) = CT A(3,3) = CT A(1,3) = -ST A(3,1) = ST A(2,2) = 1. C ASSIGN 29 TO IXFORM GO TO 600 C C************************************************************************* C C ROTATE VECTOR 1 INTO XZ PLANE [(X1,Y1,Z1) -> (X1',0,Z1)] C {Z1 SHOULD BE ZERO. SEE NEXT SECTION.} C 29 ASSIGN 30 TO IZERO GO TO 500 C 30 CONTINUE R = DSQRT(Q(1,1)**2 + Q(2,1)**2) IF (R.LT.EPS) GO TO 39 CT = Q(1,1)/R ST = Q(2,1)/R A(1,1) = CT A(2,2) = CT A(1,2) = ST A(2,1) = -ST A(3,3) = 1. C ASSIGN 39 TO IXFORM GO TO 600 C C************************************************************************* C C ROTATE VECTOR 1 ONTO X PLANE [(X1',0,Z1) -> (R1,0,0)] C {Z1 SHOULD BE ZERO. THIS SHOULD BE A NULL OPERATION} C 39 IF (DABS(Q(3,1)).LT.EPS) GO TO 700 WRITE(6,9999)EPS 9999 FORMAT('0>>>>> WARNING!! |Z-COMPONENT| OF X-VECTOR .GT. ',G12.6) WRITE(6,9998)(Q(J,1),J=1,3) 9998 FORMAT(' ',5X,'X-VECTOR:',3G16.8/) C ASSIGN 40 TO IZERO GO TO 500 C 40 CONTINUE R = DSQRT(Q(1,1)**2 + Q(3,1)**2) IF (R.LT.EPS) GO TO 49 CT = Q(1,1)/R ST = Q(3,1)/R A(1,1) = CT A(3,3) = CT A(1,3) = ST A(3,1) = -ST A(2,2) = 1. C ASSIGN 49 TO IXFORM GO TO 600 C 49 GO TO 700 C C*************************************************************************** 500 CONTINUE C C ZERO OUT =A= C DO 510 I = 1,3 DO 510 J = 1, 3 510 A(I,J) = 0. C GO TO IZERO C C*************************************************************************** 600 CONTINUE C C TRANSFORM =Q= C DO 625 IC = 1,3 C DO 605 KK = 1,3 TMP(KK) = 0. 605 CONTINUE C DO 615 IR = 1, 3 DO 610 L = 1,3 TMP(IR) = TMP(IR) + A(IR,L)*Q(L,IC) 610 CONTINUE 615 CONTINUE C DO 620 IR = 1, 3 Q(IR,IC) = TMP(IR) 620 CONTINUE C 625 CONTINUE C GO TO IXFORM C C*************************************************************************** 700 RETURN END C BLOCK DATA ATOMS IMPLICIT REAL*8 (A-H,O-Z) C DIMENSION ATWT(86) COMMON/ATMDAT/AN, ATWT C DATA ATWT/ & 1.00797, 4.0026, 6.939, 9.0122, 10.811, & 12.01115, 14.0067, 15.9994, 18.9984, 20.183, & 22.9898, 24.312, 26.9815, 28.086, 30.9738, & 32.064, 35.453, 39.948, 39.102, 40.08, & 44.956, 47.90, 50.942, 51.996, 54.938, & 55.847, 58.933, 58.71, 63.54, 65.37, & 69.72, 72.59, 74.922, 78.96, 79.909, & 83.80, 85.47, 87.62, 88.905, 91.22, & 92.906, 95.94, 98., 101.07, 102.905, & 106.4, 107.870, 112.40, 114.82, 118.69, & 121.75, 127.60, 126.904, 131.30, 132.905, & 137.34, 138.91, 140.12, 140.907, 144.24, & 147., 150.35, 151.96, 157.25, 158.924, & 162.50, 164.930, 167.26, 168.934, 173.04, & 174.97, 178.49, 180.948, 183.85, 186.2, & 190.2, 192.2, 195.09, 196.967, 200.59, & 204.37, 207.19, 208.98, 210., 210., & 222./ C DATA AN/6.02252/ C END ===================================================================== From: IN%"jstewart@fai.com" " (Dr. James Stewart)" 14-FEB-1994 19:09:34.10 Please feel free to use the symmetry codes in MOPAC 7, the public-domain program. The routine SYMTRZ plus its dependent routines, can identify most symmetry axes. It fails on C60 and some other high-symmetry species. Jimmy Stewart ===================================================================== From: IN%"NEDWED@ptc.tu-graz.ac.at" "Dipl.-Ing. Karl NEDWED" Dear Dr. Savary, there is a fairly easy way to determine the principal axes of a molecule, indeed. In fact, each symmetry element (or operation) can be described by a single axis. For proper or improper rotations it is of course the axis itself, ` for mirror planes the normal axis to the plane. I am currently programming a software packet named "SYMAPPS for Windows" that ` determines the point group of a molecule automatically, once the atomic coordinates have been defined (if via absolute Cartesian or internal does not ` matter, the program converts internal to absolute coordinates anyway). To find the point group, all principal axes (and all the other defining axes too) have to be determined, so I developed a suitable algorithm. I will send you the preprint of a paper which is due to be published soon. If you are interested in the software (a beta demo version is available), just send me a mail. Yours very truly Karl NEDWED Institute for Physical and Theoretical Chemistry Graz Institute of Technology Rechbauerstr. 12 A-8010 Graz Austria phone: +316 873 8231 e-mail: nedwed@ptc.tu-graz.ac.at ===================================================================== Note I have personaly contact Karl Nedwed and I have received a copy of his program SYMAPPS 2.0, although it is now at the stage of a late beta version it works fine As we discussed it with each other, Karl has put a demo version to the net. Also he should publish a paper soon. ===================================================================== Dear netters, Within the last few years there have piled up requests how to determine point groups of molecules automatically, i.e. with a computer. A number of methods have been developed, but they all lack either applicability to a computer or suitability to determine all existing point groups. A computer program is needed that * determines the point group of molecules automatically in a reasonable time, * lets point group determinations pe performed, even of distorted molecules(!), * lets multiple point group determinations of the same molecule be performed, each one with a different allowance of distortion. We have been working on this problem for a year now and are proud to present a software that will do ALL THIS for you and and a lot more. The computer program is called SYMAPPS for Windows and runs on IBM PC or compatible systems under MS Windows(R). The main features are: * Input of molecular data via absolute (Cartesian) coordinates. * Input of molecular data via internal (Z-matrix) coordinates. * Automatic point group determinations of any molecule. Neither the size of the molecule nor the detected point group is subject to any restrictions (apart from computer memory). The extent of distortion can be gauged by a so-called uncertainty parameter T, which can be chosen from 0 to about 0.7. The greater T, the greater the distortion of the molecule may be in order to still find an idealized point group of high symmetry. For example, if a particular compound shows a Jahn-Teller-Effect, with a small value of T the point group D4h will be found, while for larger values of T the group Oh will occur. It is the user's task to decide, if in his computations the distortion is too large to use Oh or not. In any case, the extent of distortion can be gauged by the absolute value of T. * Visualization of molecules in a three-dimensional, perspective outline mode on screen. Only bonds and atom identifiers are displayed in this mode. Real time rotating and resizing is possible. * Visualization of molecules in the three-dimensional perspective spacefill mode on screen, where atoms assume spherical shapes. * Display of the character tables of arbitrary point groups (not restricted to the 32 crystallographic ones). * Reduction of reducible representations into their irreducible components. SYMAPPS for Windows will be of great use to chemists physicists and crystallographers, involved in both research and teaching. For a demo version, please contact ***Karl NEDWED ***Institute for Physical and Theoretical Chemistry ***Graz Institute of Technology ***A-8010 Graz ***Austria ***E-mail address: nedwed@ptc.tu-graz.ac.at or simply ftp it from ***server: ftp.tu-graz.ac.at ***login: anonymous ***password: your E-mail address ***directory: pub\msdos\symapps The full version will be available soon. A single user edition will be US$100 (excl. 20% VAT and delivery), for site licenses please contact us. We hope that SYMAPPS for Windows will simplify a lot of time-consuming computations and determinations in laboratories. ===================================================================== From: IN%"wendy@cumbnd.bioc.columbia.edu" "wendy chen" 14-FEB-1994 21:36:12.26 you can simply calculate the moments of inertial tensor with mass=1 for every atom. the eigenvectors of the tensor matrix are the corresponding principle axes. hope this helpful! wendy chen ===================================================================== From: IN%"CBAS25@VAXA.STRATHCLYDE.ac.uk" "CBAS25 ::P_BLADON ::CBAS25" 15-FEB-1994 00:14:05.30 Dear Francois, I have made an addition to MOPAC-6 which may do what you want. I puts out the Cartesian coordinates of the molecule in a coordinate frame defined by the principal axes. It also allows the output of the moments of inertia and the dipole moment's components in the same frame. Yours sincerely, Peter Bladon ===================================================================== From: IN%"deloff@sc2a.unige.ch" 15-FEB-1994 10:25:42.98 Salut, j'ai recu la bibliographie: les 2 premiers me semblent interessants. As-tu recu des reponses ? a bientot, ciao Andre >L4 ANSWER 1 OF 5 CA COPYRIGHT 1994 ACS >AN CA113(11):96655t CA > Correction of: CA112(23):215706b >TI Computer perception of constitutional (topological) ***symmetry*** > : TOPSYM, a fast algorithm for partitioning atoms and pairwise > relations among atoms into equivalence classes >AU Ruecker, Gerta; Ruecker, Christoph >CS Inst. Org. Chem. Biochem., Univ. Freiburg >LO Freiburg D-7800, Fed. Rep. Ger. >SO J. Chem. Inf. Comput. Sci., 30(2), 187-91 >SC 20-5 (History, Education, and Documentation) >DT J >CO JCISD8 >IS 0095-2338 >PY 1990 >LA Eng >OS CJACS >AB An algorithm for the perception of constitutional symmetry in mols. > (graphs) is presented that partitions not only atoms (vertices) but > also all pairwise relations among skeleton atoms into equivalence > classes. The method works without canonical numbering, essentially > by raising the connectivity matrix of the arbitrarily numbered mol. > (graph) to its 2nd, 3rd, etc., power and evaluating the entries in > these higher order matrixes. > >L4 ANSWER 2 OF 5 CA COPYRIGHT 1994 ACS >AN CA112(23):215706b CA >TI Computer perception of constitutional (topological) ***symmetry*** > : TOPSYM, a fast algorithm for partitioning atoms and pairwise > relations among atoms into equivalence classes >AU Ruecker, Gerta; Ruecker, Christoph >CS Inst. Org. Chem. Biochem., Univ. Freiburg >LO Freiburg D-7800, Fed. Rep. Ger. >SO J. Chem. Inf. Comput. Sci., 30(2), 187-91 >SC 20-5 (History, Education, and Documentation) >DT J >CO JCISD8 >IS 0095-2338 >PY 1990 >LA Eng >OS CJACS >AB An algorithm for the perception of constitutional symmetry in mols. > (graphs) is presented that partitions not only atoms (vertices) but > also all pairwise relations among skeleton atoms into equivalence > classes. The method does not require canonical numbering by raising > the connectivity matrix of the arbitrarily numbered mol. (graph) to > its 2nd, 3rd, etc., power and evaluating the entries in these higher > ordered matrixes. The computer program based on this algorithm > (TOPSYM), written in FORTRAN, is described and used to depict mol. > structures from the constitutional formula of the compd. as the only > input. > >L4 ANSWER 3 OF 5 CA COPYRIGHT 1994 ACS >AN CA112(10):88800a CA >TI CRYST - a system to display 3D images of crystal structure, > ***symmetry*** operations and crystal forms >AU Sakurai, Tosio; Kobayashi, Kimiko; Horiki, Tsuyoshi; Furukawa, > Masao; Naitou, Kimitoshi >CS Fac. Educ., Shinshu Univ. >LO Nagano 380, Japan >SO J. Appl. Crystallogr., 22(6), 633-9 >SC 75-10 (Crystallography and Liquid Crystals) >DT J >CO JACGAR >IS 0021-8898 >PY 1989 >LA Eng >AB CRYST is a 3D computer graphics program to help the understanding of > crystallog. procedures. The 3-dimensional image of a crystal > structure is displayed, together with the arrangement of the > symmetry elements in the unit cell. The symmetry-related atoms can > be generated successively on a graphics screen by designating > symmetry elements with a pen and tablet. Changes in morphol. of a > growing crystal may also be drawn by computer. Several applications > of the system are described. > >L4 ANSWER 4 OF 5 CA COPYRIGHT 1994 ACS >AN CA107(13):111717m CA >TI ***Symmetry*** control in reactions in molecular cavities >AU Guarino, A. >CS Ist. Chim. Nucl., CNR >LO Rome 00036, Italy >SO J. Mol. Graphics, 5(1), 22-4, 28 >SC 7-4 (Enzymes) >DT J >CO JMGRDV >IS 0263-7855 >PY 1987 >LA Eng >AB Multistep reaction processes which occur in mol. cavities, like > those involved in host-guest inclusion compds., have been found to > depend on the fulfilment of certain symmetry requirements; > similarly, a symmetry control is obsd. whenever mol. cavities are > formed by the active sites of specific enzyme-substrate complexes. > It seems reasonable to suggest that, if the enzymic structures are > known, a careful use of these simple symmetry considerations may > contribute to a better interpretation of the reactivity-structure > correlations obtained by computer aided mol. graphic models of these > enzymic complexes. > >=> s > ====================================================================== Adresse: Telephone: E-mail: Andre DELOFF 702 64 70 deloff@scsun.unige.ch Services Informatiques 702 65 77 deloff@sc2a.unige.ch Universite de Geneve Sciences II, b. 459 30, Quai Ernest Ansermet 1211 Geneve 4 ===================================================================== ===================================================================== From: IN%"J63C002@HUSZEG11.bitnet" "J63C002" 15-FEB-1994 17:31:54.39 Dear netters There exists a program recognizing molecular orbital symmetries which can determine the principal axes of an arbitrary molecule, too. This is the program No. 484, available at QCPE (Quantum Chemistry Program Exchange). You can find the description of this program in the QCPE Bulletin 4(4), 107(1984) and Comp. & Chem. 9, 179(1985). The program is well documented and very simple to use. For determination the molecular symmetry you have to write into the input file the cartesian coordinates of the molecule. ===================================================================== From: IN%"jxh@ibm12.biosym.com" " (Joerg Hill)" 16-FEB-1994 01:37:36.58 Since a direct answer does not work: Knowing only the atomic coordinates there is no way to find the prinicipal axes of symmetry. You need at least still the information which atoms are the same (in sense of symmetry). You can take atomic symbols, masses, atomic charges or something like that. With this information it is very easy to obtain the desired information. All physical properties of the molecule have to be invariant to the application of a symmetry operation. That means if you calculate e. g. the principal axes of inertia of your molecule (where you need the masses for), the principial axis of symmetry must be one of these axes (the other symmetry elements you can obtain in this way, too). There is a variety of programmes which does this. I know Gaussian and Turbo- mole. Joerg-R. Hill ===================================================================== From: IN%"jxh@ibm12.biosym.com" " (Joerg Hill)" 16-FEB-1994 20:39:19.61 Since there is obviously an interest in learning something about how to determine point groups with a computer programme here my DM 0.034 (=$0.02): All physical properties of a molecule have to be invariant to the application of a symmetry operation. If we consider an easy to calculate property such as the inertia tensor of the molecule we see first that all symmetry elements must pass the centre of gravity. If we diagonalize the inertia tensor we get three moments of inertia (eigenvalues) and three principal axes of inertia (eigenvectors). Now we can distinguish some cases: 1) one moment of inertia is zero, the others not --> the molecule is linear, possible point groups C*v or D*h (the * stands for infinite), check by comparing the atoms 2) all three moments of inertia are different (asymmetric top molecules) --> no axes of order greater than 2 are possible, point groups D2h, D2, C2v, C2h, C2, Ci, Cs, and C1, if at least one of the principal axes is C2 you have either D2h (all principal axes are C2 and an inverson centre exists), D2 (as D2h, but no inverson centre), C2v, C2h, or C2; otherwise you have Ci, Cs, or C1. 3) two moments of inertia are the same, the third is different (symmetric top molecules) --> all axial point groups except the cubic ones (T, Td, Th, O, Oh, I, Ih) are possible, your unique principal axis of inertia is one rotation axis and you can further distinguish by comparing sets of atoms. 4) all three moments of inertia are the same (spherical top molecules) --> possible point groups T, Td, Th, O, Oh, I, Ih and you have a problem ! It is not possible to obtain a rotation axis from the inertia tensor (where is top or bottom of a sphere ?) But you can check sets of atoms. Since each symmetry element has to pass through the centre of gravity you can calculate the distance atom from the centre of gravity and if you find a set of atoms of the same element with the same distances from the centre of gravity you have found a rotation axis. Note: There are a few cases of so-called accidiental spherical top molecules which do not belong to a cubic point group. These are hard to handle, but rare, too. OK, that's the basic algorithm. Literature for this is rare. Most textbooks only deal with symmetry operations, point groups etc., but not with how to get this into a running programme. I only remember an anchient spectroscopy textbook, which explained somewhat of this algorithm, but I can't cite it. Available codes are basically Turbomole, which uses all this stuff to speed up calculations, since you can reduce the computional effort by the order of the point group. Joerg-R. Hill ===================================================================== From: IN%"rgab@purisima.molres.org" "R.G.A.Bone" 17-FEB-1994 00:35:33.67 Concerning the various perspectives on deducing the geometric symmetry of a molecule from its nuclear coordinates: i) The Gaussian package readily does this, (one of its more irritating features I should add), though you can turn symmetry off with a whole manner of flags at the various levels of calculation, you know, dep- ending on how you want to "fix" your result (cf. 'symmetry-broken' solutions in UHF). ii) Philosophically (regrettably) given that assemblies of nuclei (i.e., molecules) are not static - there are continuous vibrations, etc., the only molecules which will have any geometric symmetry at all, at any instant, are triatomics (a plane of symmetry) and diatomics. The latter will have the infinite-fold rotation axis (and a whole "bunch" of others if homonuclear). Thus, only if two nuclei have symmetry-related coordinates (to some arbitrary level of precision) is geometric symmetry present. Of course, one could specify this level of precision to be the dimension of a nucleus (typically femtometres). But, being chemists, with an under- standing of spectroscopy, we know a little better and assume that, for all intents and purposes point-symmetry operations commute with the vibronic Hamiltonian so this issue does not arise and the 'time-averaged' position of the nuclei, or the geometry at the well in the potential is what counts. iii) But, if you are a computer, to examine a number of nuclear coordinates and determine symmetric-relationships between them requires some intell igent decision concerning what is "near-symmetry" and what is "exact- symmetry". Suppose there are small rounding errors in the data: e.g., 2 nuclear positions: 1.00000000 0.50000000 2.34567890 1.00000000 0.50000000 -2.34567889 Are these 2 nuclei symmetrically-related? Well, surely yes, although their z-coordinates differ by a trivial amount. The algorithm must contain a threshold-cutoff which copes with cases like this. iv) In response to the comment that you need to know the nuclear identity as well as the coordinates in order to deduce symmetry. Well, except for the trivial case of diatomics, I challenge anybody to find 2 nuclei in a molecule which are NOT identical but which are in exactly-symmetry- related coordinates, to say 10^-6 Angstrom precision. Of course, there may be circumstances under which it is desirable to label (for example iso- topic) substituents as symmetrically-equivalent, and cases where it is not. But that's moving the goal-posts. It also depends on the source of the data: is it an experimental or theoretical geometry for the isotopomer? (i.e., have zero-point effects been included or not ?) Basically, this matter of deducing the point group from a set of coordinates does have a slight algorithmic difficulty, which is perhaps why it has not been widely implemented. Arguably also, let's face it: almost all molecules on this planet don't have any symmetry at all; (theoretical) chemists' obsession with symmetry comes from 1) the small size of molecules they are accustomed to dealing with (symmetry is more preponderent in small molecules), 2) the fact that, even for small molecules, use of symmetry can make a big calculation more practical. Furthermore, there are hardly any molecules for which the point group can't be deduced "by inspection", unless there happens to be a potential confusion between "near-symmetry" and actual-symmetry. One might argue that that difficulty increases as molecules increase in size, but then the amount of symmetry typically decreases in the same way (crystal-lattice unit-cells, excepted). Richard Bone ===================================================================== R. G. A. Bone. Molecular Research Institute, 845 Page Mill Road, Palo Alto, CA 94304-1011, U.S.A. Tel. +1 (415) 424 9924 x110 FAX +1 (415) 424 9501 E-mail rgab@purisima.molres.org ------------------------------------------------------------------------------- --------------------- Every Theory has its "Grassy Knoll" --------------------- ------------------------------------------------------------------------------- ===================================================================== From GOVENDEM@che.und.ac.za Wed Mar 30 04:02:27 1994 Received: from owl.und.ac.za for GOVENDEM@che.und.ac.za by www.ccl.net (8.6.4/930601.1506) id DAA25161; Wed, 30 Mar 1994 03:16:19 -0500 Received: from charon1.cc.und.ac.za by owl.und.ac.za with SMTP (PP) id <01116-0@owl.und.ac.za>; Wed, 30 Mar 1994 10:15:46 +0200 Received: From CSD/WORKQUEUE by charon1.cc.und.ac.za via Charon-4.0A-VROOM with IPX id 100.940330101509.320; 30 Mar 94 10:15:43 -0200 Message-ID: From: GOVENDEM To: chemistry@ccl.net Date: Wed, 30 Mar 1994 10:14:41 +0200 (SAST) Subject: Help: With BSSE calculation using Monstergauss X-pmrqc: 1 Priority: normal X-mailer: PMail v3.0 (R1a) Dear Netters, We are trying to calculate the interaction energies using Morukuma energy decomposition analysis, however the CT(charge transfer) and Pol(polorization term) have no Counterpoise correction values. Could anyone provide info regarding this problem. How does the monomer part of the energies contribute to such a calculation or is it included in finding the interaction energies. Many thanks ______________________________________________________________________ M.G. Govender Centre for Theoretical and Computational Chemistry Dept of Chemistry University of Natal King George V Avenue Durban South Africa ______________________________________________________________________ From MURASHOV@ac.dal.ca Wed Mar 30 11:02:15 1994 Received: from SYSWRK.UCIS.DAL.CA for MURASHOV@ac.dal.ca by www.ccl.net (8.6.4/930601.1506) id KAA28356; Wed, 30 Mar 1994 10:04:54 -0500 From: Received: from AC.Dal.Ca by SYSWRK.UCIS.DAL.CA (PMDF V4.2-14 #2545) id <01HAKX7URD34004BRV@SYSWRK.UCIS.DAL.CA>; Wed, 30 Mar 1994 11:03:54 -0400 Received: from AC.DAL.CA by AC.DAL.CA (PMDF V4.2-14 #2545) id <01HAKX77Z9EO009LXA@AC.DAL.CA>; Wed, 30 Mar 1994 11:03:35 -0400 Date: Wed, 30 Mar 1994 11:03:35 -0400 Subject: re:fungus To: chemistry@ccl.net Message-id: <01HAKX781XV6009LXA@AC.DAL.CA> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters! Not so long ago I posted a request for "FUNGUS" MD codes. I would like to thank all who responded to me. Here some solid state MD sources: FUNGUS - available from Prof.C.R.A.Catlow e-mail:richard@ricx.ri.ac.uk MDCSPC2 - available from Dr.W.Smith e-mail:W.Smith@dl.ac.uk MolDy - available from Dr.K.Refson e-mail:Keith.Refson@earth.ox.ac.uk From schuetz@ips.id.ethz.ch Wed Mar 30 11:19:01 1994 Received: from bernina.ethz.ch for schuetz@ips.id.ethz.ch by www.ccl.net (8.6.4/930601.1506) id KAA28694; Wed, 30 Mar 1994 10:38:53 -0500 Received: from sitter (actually sitter.ethz.ch) by bernina.ethz.ch with SMTP inbound; Wed, 30 Mar 1994 17:38:51 +0200 Received: from doubs.zurich by sitter id AA01936; Wed, 30 Mar 94 17:38:51 +0200 Received: by doubs.zurich (5.0/SMI-SVR4) id AA07412; Wed, 30 Mar 1994 17:38:47 --100 From: schuetz@ips.id.ethz.ch (Martin Schuetz) Message-Id: <9403301538.AA07412@doubs.zurich> Subject: AVS chemistry viewer... To: chemistry@ccl.net Date: Wed, 30 Mar 1994 17:38:45 +0200 (MET DST) X-Mailer: ELM [version 2.4 PL20] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 769 Dear netters, Is there anybody out there who has already tried to build a new input reader module on top of MSI's AVS chemistry viewer (a module which generates the same output as the g92reader or the MOPAC reader but for different input file formats) ? Is there an ftp archive site for AVS modules besides avs.ncsc.org which focuses on chemical applications ? To keep the net traffic small please mail directly to me, I'll summarize if there is any general interest. With kind regards M.Schuetz -- Martin Schuetz Phone: +41 1 256 55 66 Interdisciplinary Project Center FAX: +41 1 261 04 68 for Supercomputing, ETH Zuerich Switzerland E-mail: schuetz@ips.id.ethz.ch or mgs@ips.id.ethz.ch From mls@wucmd.wustl.edu Wed Mar 30 12:02:49 1994 Received: from wugate.wustl.edu for mls@wucmd.wustl.edu by www.ccl.net (8.6.4/930601.1506) id LAA29240; Wed, 30 Mar 1994 11:33:53 -0500 Received: by wugate.wustl.edu (5.67b+/WUSTL-0.3) with SMTP id AA27956; Wed, 30 Mar 1994 10:33:47 -0600 Received: by wucmd (920330.SGI/911001.SGI) for @wugate.wustl.edu:chemistry@ccl.net id AA02981; Wed, 30 Mar 94 10:10:05 -0600 Date: Wed, 30 Mar 94 10:10:05 -0600 From: mls@wucmd.wustl.edu (Mark Smythe) Message-Id: <9403301610.AA02981@wucmd> To: chemistry@ccl.net Subject: Enzyme-inhibit. complexes Dear CCL'ers I would like to obtain coordinates of enzyme-inhibitor complexes (X-Ray diffraction studies). In addition, I would like the affinity of the inhibitor for its receptor. I have retrieved several examples from the brookhaven database, but I am sure that there must be a lot more, particulary in industry. If anyone has additional examples, that are not in the brookhaven database, and are willing to share them, please let me know. Thanks Mark ----------------------------------------------------------------------------- | Mark Smythe | Phone : CMD (314) 935 4683 | | Centre for Molecular Design | Fax : (314) 935 4979 | | Washington University | Phone : Lab (314) 362 2987 | | Lopata Hall, Box 1099, One Brookings | | | Drive, St Louis, Mo, 63130 | E-Mail: mls@wucmd.wustl.edu | ----------------------------------------------------------------------------- From casida@CHIMCN.UMontreal.CA Wed Mar 30 12:07:04 1994 Received: from condor.CC.UMontreal.CA for casida@CHIMCN.UMontreal.CA by www.ccl.net (8.6.4/930601.1506) id LAA29542; Wed, 30 Mar 1994 11:55:51 -0500 Received: from chims1.CHIMCN.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA13535 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Wed, 30 Mar 1994 11:25:14 -0500 Received: by chims1.CHIMCN.UMontreal.CA (930416.SGI/5.17) id AA14414; Wed, 30 Mar 94 11:29:03 -0500 From: casida@CHIMCN.UMontreal.CA (Casida Mark) Message-Id: <9403301629.AA14414@chims1.CHIMCN.UMontreal.CA> Subject: STO program To: CHEMISTRY@ccl.net Date: Wed, 30 Mar 1994 11:29:02 -0500 (EST) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1254 Greetings! I hope that this isn't a FAQ. If so, please send all flames to me. We are writing some routines involving integrals over STOs and would like to check our work against other code. Where could we obtain free FORTRAN code for an atomic (say) HF STO program? ... Mark -- *-------------------------------------------------------* | Mark E. Casida | | Chemistry Computing Professional | |-------------------------------------------------------| | B-605 Pavillon principal | | Departement de chimie \_____/ | | Universite de Montreal /\0|0/\ | | Case postale 6128 | | | | | | Succursale centre-ville \/ \/ | | Montreal, Quebec H3C 3J7 -----"-"---- | | Canada | |-------------------------------------------------------| | tel: (514) 343-6111 poste/extension 3901 | | e-mail: casida@chimcn.umontreal.ca | | fax: (514) 343-2468 | *-------------------------------------------------------* From davis@nod.bms.com Wed Mar 30 12:10:53 1994 Received: from CLIFF.BMS.COM for davis@nod.bms.com by www.ccl.net (8.6.4/930601.1506) id LAA29551; Wed, 30 Mar 1994 11:56:10 -0500 Received: from nod (nod.bms.com) by cliff.bms.com (PMDF #2529 ) id <01HAKZ3Z5V7K0000BS@cliff.bms.com>; Wed, 30 Mar 1994 11:58:03 EST Received: by nod (920330.SGI/920502.SGI) for @cliff.bms.com:Chemistry@ccl.net id AA25211; Wed, 30 Mar 94 11:55:51 -0500 Date: 30 Mar 1994 11:55:51 -0500 From: davis@nod.bms.com (Malcolm Davis) Subject: Using SGI's IRIS Explorer in Computational Chemistry To: Chemistry@ccl.net Message-id: <9403301655.AA25211@nod> X-Envelope-to: Chemistry@ccl.net Content-transfer-encoding: 7BIT I have been looking at using SGI's IRIS Explorer (IE) for chemistry visualization and would be interested in hearing from anyone else who has looked into IE as a visualization tool. My biggest concern with IE is the standard chemistry data type. It seems to have been added as an afterthought without sufficient consideration to the wide range of uses that computational chemists might have for such a tool. I would like to stimulate a discussion hopefully leading to a new standard data type (whether official or de facto), but I am not sure of the best forum for such a discussion. This mailing list is certainly out of the question for such a narrow interest topic. The newsgroup comp.graphics.explorer would seem most natural and is not flooded with other discussions, but an earlier message of mine there did not elicit a large response. So I am open to suggestions. I look forward to hearing from you if you are interested in the topic. Sincerely, Malcolm Davis P.S. If a discussion does get started somewhere, I will post instructions on how to take part. -- Malcolm E. Davis USMail: Macromolecular Modeling Bristol-Myers Squibb P.O.Box 4000 Princeton, NJ 08543-4000 Email : davis@nod.bms.com Phone : 609-252-4324 FAX : 609-252-6030 Office: LV H.3812 From JARZECAA@ctrvax.Vanderbilt.Edu Wed Mar 30 13:02:40 1994 Received: from ctrvx1.Vanderbilt.Edu for JARZECAA@ctrvax.Vanderbilt.Edu by www.ccl.net (8.6.4/930601.1506) id MAA00149; Wed, 30 Mar 1994 12:29:56 -0500 From: Received: from ctrvax.Vanderbilt.Edu by ctrvax.Vanderbilt.Edu (PMDF V4.2-15 #3899) id <01HAKXYOBKXS8XZID0@ctrvax.Vanderbilt.Edu>; Wed, 30 Mar 1994 11:26:47 CST Date: Wed, 30 Mar 1994 11:26:47 -0600 (CST) Subject: Internal Coordinates in Gaussian To: CHEMISTRY@ccl.net Message-id: <01HAKXYOFBYQ8XZID0@ctrvax.Vanderbilt.Edu> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Netters, For a long time I have been looking for the FORTRAN program which would read the Gaussian's frequency, forces and displacement of atoms in Cartesian coordinates and transform them to the specific (defined by a user) internal coordinates of a molecule. I know that some internal coordinates are available in Gaussian by construction of a z-matrix, but the most of them are not. The classical example for a coordinate, which one cannot define by a z- matrix, is a triangle with three lengths as internal coordinates. To define the triangle in a z-matrix one has to use two lengths and an angle. There is no way to use three lengths by a z-matrix in this situation. I ask You if one knows any programs or at least references that could solve or help me to solve my problem. Thank you for your time and help. Andrzej A. Jarzecki ***************************************** Andrzej A. Jarzecki Vanderbilt University Department of Chemistry Nashville, TN 37235. Telenone: 615-322-7324 e-mail: Jarzecaa@Ctrvax.Vanderbilt.Edu ***************************************** From doherty@msc.edu Wed Mar 30 13:06:52 1994 Received: from noc.msc.edu for doherty@msc.edu by www.ccl.net (8.6.4/930601.1506) id MAA29758; Wed, 30 Mar 1994 12:10:29 -0500 Received: from uh.msc.edu by noc.msc.edu (5.65/MSC/v3.0.1(920324)) id AA10344; Wed, 30 Mar 94 11:08:08 -0600 Received: from mac3.msc.edu by uh.msc.edu (5.65/MSC/v3.1r(920220)) id AA06007; Wed, 30 Mar 94 11:08:04 -0600 Message-Id: <9403301708.AA06007@uh.msc.edu> X-Sender: doherty@uh.msc.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 30 Mar 1994 11:08:07 -0600 To: chemistry@ccl.net From: doherty@msc.edu (David C. Doherty) Subject: XMol: WWW, RS/6000 version Cc: xmol@msc.edu, doherty@msc.edu Minnesota Supercomputer Center, Inc. (MSCI) is pleased to make two announcements: 1. We have made the XMol User Guide available via World Wide Web (WWW). To access this document from one of the various flavors of Mosaic (X, Mac, Win), open the following Universal Resource Locator (URL) from the File Menu: http://www.arc.umn.edu/GVL/Software/xmol/XMol.html 2. In response to very heavy demand, we have now made available an RS/6000 version of XMol. Some of you have already noticed its availability, and a few users have reported some spurious error messages when running it under certain conditions. We believe that these messages, which don't affect the running of XMol, are due to problems in the AIX Motif libraries, for which we do not have source code. As always, XMol may be anonymous ftp'ed from: ftp://ftp.msc.edu/pub/xmol Get the README file for downloading and installation instructions. It is now also possible to download it via the WWW Server listed above. One final note: Among the conditions under which we make XMol freely available is the condition that we remain its sole distributor. In order to ensure that XMol remains freely available, please abide by this restriction and do not make it available for redistribution via anonymous ftp, gopher, WWW, etc. A full description of the conditions under which XMol is released is contained in the README file. Please read it. Comments and suggestions should be directed to xmol@msc.edu. Thanks for listening, and happy XMol'ing! Dave Doherty --- David C. Doherty Minnesota Supercomputer Center, Inc. doherty@msc.edu From CHEM8@vax.york.ac.uk Wed Mar 30 13:10:42 1994 Received: from leeman.york.ac.uk for CHEM8@vax.york.ac.uk by www.ccl.net (8.6.4/930601.1506) id MAA29984; Wed, 30 Mar 1994 12:23:51 -0500 Via: uk.ac.york.vax; Wed, 30 Mar 1994 17:57:26 +0100 Date: Wed, 30 Mar 94 18:02 BST From: "John Waite, Tel 1-7238958, N.H.R.F., Vas. Konstantinou 48, Athens 116-35" To: CHEMISTRY Subject: CENTRAL and EASTERN EUROPEAN CHEMISTS Message-ID: <"leeman.yor.195:30.02.94.16.57.28"@york.ac.uk> Athens, 30th March 1994 Hi Central and Eastern European Chemists, The European Community budget for 1994 foresees supporting the participation of organizations and/or scientists from Central and Eastern Europe in the projects of a number of specific Community programmes under the Third Framework Programme. Further information man be obtained from: European Commission, DG XII, Science, Research and Development - Joint Research Centre, Central and Eastern Europe, Rue de la Loi, 200 B-1049 Brussels, Belgium Phone: ++32-2-295-66-49 Fax: ++32-2-296-33-08 THEORETICAL OR COMPUTATIONAL CHEMISTS REQUIRED FOR PARTICIPATION IN A EUROPEAN COMMUNITY FUNDED PROJECT We participate in such a programme and are asking for a suitable researcher to work on the calculation and analysis of electronic nonlinear optical properties (polarizabilities first and second hyperpolarizabili-ties) of organic and transition metal or ganometallic compounds by semi-empirical and ab-initio methods. This person should have already completed his Ph.D (doctorate) and preferably have some experience at least in the use of ab-initio and semi-empirical methods. An adequate knowledge of English is considered necessary. To apply please forward a curriculum vitae, a letter of recommendation and any other appropriate material, by the end of May 1994, to: Drs M. G. Papadopoulos and J. Waite The National Hellenic Research Foundation 48 Vas. Constantinou Ave. Athens 116 35 Greece. Further information may be otained , if required, from the above or by: e-mail mpapad@isosun.ariadne-t.gr chem8@vax.york.ac.uk Phone: ++ 30-1-7238958 Fax: ++ 30-1-7246618. In addition, synthesis chemists (organo-transition metals) should contact: Prof. A. Underhill, Department of Chemistry, University College of North Wales, Bangor LL57 2UW Gwynedd, U.K. Phone: ++44-248-38-2375 Fax: ++44-248-37-0528 and measurement chemists (Non-Linear Optical Properties): Prof. D. Bloor, Department of Physics, University of Durham, Durham, U.K. From DSMITH@uoft02.utoledo.edu Wed Mar 30 14:02:12 1994 Received: from uoft02.utoledo.edu for DSMITH@uoft02.utoledo.edu by www.ccl.net (8.6.4/930601.1506) id NAA00951; Wed, 30 Mar 1994 13:20:41 -0500 Received: from UOFT02.UTOLEDO.EDU by UOFT02.UTOLEDO.EDU (PMDF V4.2-10 #5345) id <01HAL1FOF0LC000867@UOFT02.UTOLEDO.EDU>; Wed, 30 Mar 1994 13:19:21 EST Date: Wed, 30 Mar 1994 13:19:21 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Re: CCL:Using SGI's IRIS Explorer in Computational Chemistry To: davis@nod.bms.com Cc: chemistry@ccl.net Message-id: <01HAL1FOFA8I000867@UOFT02.UTOLEDO.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"davis@nod.bms.com" X-VMS-Cc: CHEMISTRY MIME-version: 1.0 Content-transfer-encoding: 7BIT Malcolm: I would suggest that AVS and its Molecule Data Type are much better for chemistry, since the data type was an integral part of the initial design of AVS. It is very flexible and as such there are many ways in which data can be stored in its various components, which are hierarchical lists. I have a nine+ page description of how the MDT is structured if anyone is interested (at least, how it is structured and used in the Chemistry Viewer). In general, the MDT is an organized collection of atom-based substructure and quantum chemical information. A more general description of the MDT is availabie in a chapter by Joe Leonard in an upcoming volume on Molecular Science in the Insights and Innovation in Data Visualization series from Manning Publications, Jack Bowie (DEC) and Art Olson (Scripps), editors. Maybe if Joe is listening he would consent to better describe the MDT by quoting from his chapter. Doug Douglas A. Smith Assistant Professor, Department of Chemistry Center for Drug Design and Development and Chairman-elect, ACS Division of Computers in Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu