From doki@indy.mars.vein.hu Mon Feb 27 03:53:13 1995 Received: from miat0.vein.hu for doki@indy.mars.vein.hu by www.ccl.net (8.6.9/930601.1506) id DAA29319; Mon, 27 Feb 1995 03:17:32 -0500 Received: by miat0.vein.hu (5.65/DEC-Ultrix/4.3) id AA14182; Mon, 27 Feb 1995 09:16:45 -0600 Received: by indy.mars.vein.hu (931110.SGI/930416.SGI.AUTO) for @miat0.vein.hu:Chemistry@ccl.net id AA19758; Mon, 27 Feb 95 09:20:07 +0100 From: "Abonyi Janos" Message-Id: <9502270919.ZM19756@indy.mars.vein.hu> Date: Mon, 27 Feb 1995 09:19:58 +0100 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: Chemistry@ccl.net Subject: calix(4)arenes Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Hi, I am intrested in calix(4)arenes. I am making molecular mechanics, dimamics calcualtion and energetical study for alkyled Calix(4)arens, but I havent got X-ray strucures. I would like to make molecular dinamics simulation in solvelt. I need some info about metods, publications, and force field parameters. I am using Cerius2, Spartan, PCMODEL and MM3. Thank you. Doki. Abonyi Janos University of Veszprem Dep. Org. Chem. Email: doki@indy.mars.vein.hu From dec@proteus.co.uk Mon Feb 27 05:53:14 1995 Received: from eros.britain.eu.net for dec@proteus.co.uk by www.ccl.net (8.6.9/930601.1506) id FAA00399; Mon, 27 Feb 1995 05:10:22 -0500 Message-Id: <199502271010.FAA00399@www.ccl.net> Received: from proteus.co.uk by eros.britain.eu.net with UUCP id ; Mon, 27 Feb 1995 10:09:01 +0000 From: David Clark Date: Mon, 27 Feb 95 09:09:40 GMT To: CHEMISTRY@ccl.net Subject: CCL: CPU time ratios Many thanks to those who responded to my query - the information was much appreciated. David David E. Clark | Proteus Molecular Design Ltd., | Tel: 01625-500555 Lyme Green Business Park, | Fax: 01625-500666 Macclesfield, Cheshire, | Email: D.E.Clark@proteus.co.uk SK11 0JL, UK | From wojnow@tiger.chem.uw.edu.pl Mon Feb 27 06:12:50 1995 Received: from tiger.chem.uw.edu.pl for wojnow@tiger.chem.uw.edu.pl by www.ccl.net (8.6.9/930601.1506) id EAA00324; Mon, 27 Feb 1995 04:54:40 -0500 Received: from chalbie.chem.uw.edu.pl by tiger.chem.uw.edu.pl (AIX 3.2/UCB 5.64/4.03) id AA05273; Mon, 27 Feb 1995 10:53:57 +0100 From: "" Date: Mon, 27 Feb 95 10:48:39 CST Message-Id: <38929.wojnow@tiger.chem.uw.edu.pl> X-Popmail-Charset: English To: chemistry@ccl.net Subject: need Ip1,Ip2,A1,A2 of biphenyl and its derivatives Hi netters ! I'm looking for values of first and second ionisation potentials and electon affinities of benzene and biphenyl and their simple derivatives with chlorides,alkils etc. I'll be very grateful for any references Wojtek Nowaczek wojnow@tiger.chem.uw.edu.pl Wojtek Nowaczek wojnow@tiger.chem.uw.edu.pl From savary@sc2a.unige.ch Mon Feb 27 06:18:47 1995 Received: from UNI2B.UNIGE.CH for savary@sc2a.unige.ch by www.ccl.net (8.6.9/930601.1506) id EAA00333; Mon, 27 Feb 1995 04:54:55 -0500 Received: from PCC2333F (129.194.51.63) by uni2b.unige.ch (PMDF V4.3-8 #2502) id <01HNJI8K8MSG0000ST@uni2b.unige.ch>; Mon, 27 Feb 1995 10:54:33 WET-DST Date: Mon, 27 Feb 1995 10:54:31 +0100 From: savary@sc2a.unige.ch (Francois Savary) Subject: extended hueckel on transition metal X-Sender: savary@sc2a.unige.ch To: CHEMISTRY@ccl.net Message-id: <01HNJI8KP8SI0000ST@uni2b.unige.ch> X-Envelope-to: CHEMISTRY@ccl.net MIME-version: 1.0 X-Mailer: Windows Eudora Version 1.4.4 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Hi there CCLers, I was wondering if someone out there knows of the existence of a review article on Extended Hueckel calculations on transition metals, with or without ASED corrections. If someone has a bibliography work on the subject, I would be also very much interested. Thank you in advance. I will summarize to the net if asked. Francois Savary ---------------------------------------------------------------------------- Francois Savary University of Geneva Department of Physical Chemistry CHIFI Weber 30 quai Ernest-Ansermet CH-1211 Geneva 4 Lab : 112 Phone : +4122 702 65 32 Fax : +4122 702 65 18 e-mail : savary@sc2a.unige.ch HTML : http://scsg9.unige.ch/tabmat.html (in french) : http://scsg9.unige.ch/eng/toc.html (in english) ---------------------------------------------------------------------------- From cwm@proteus.co.uk Mon Feb 27 09:57:28 1995 Received: from eros.britain.eu.net for cwm@proteus.co.uk by www.ccl.net (8.6.9/930601.1506) id JAA02606; Mon, 27 Feb 1995 09:26:16 -0500 Received: from proteus.co.uk by eros.britain.eu.net with UUCP id ; Mon, 27 Feb 1995 14:25:37 +0000 From: Chris Murray Message-Id: <9502271406.ZM13268@Ivory.proteus.co.uk> Date: Mon, 27 Feb 1995 14:06:54 +0000 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: protein xray software Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 The design of inhibitors to fit crystallographically determined protein structures often seems to assume that the structures are fixed. However there should be quite alot of information in the isotropic thermal parameters and the original diffraction data which could guide the designer about where to focus his/her designs in the first place. It ought to be possible also to represent this information graphically. Does anybody know of any software that does this? I will summarise if there is any interest. Chris Murray Proteus Molecular Design Ltd UK From steve@carbo.chem.binghamton.edu Mon Feb 27 14:53:26 1995 Received: from carbo.chem.binghamton.edu for steve@carbo.chem.binghamton.edu by www.ccl.net (8.6.9/930601.1506) id OAA09232; Mon, 27 Feb 1995 14:01:32 -0500 Received: by carbo.chem.binghamton.edu (931110.SGI/931108.SGI.ANONFTP) for chemistry@ccl.net id AA25862; Mon, 27 Feb 95 13:54:28 -0500 Date: Mon, 27 Feb 1995 13:49:22 -0500 (EST) From: Steven Schafer Subject: Q: Drug Design? To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know if there are any drugs that have been designed with computer techniques and are now legally availible in the marketplace? If so what are they and how were they designed? Any info or refrences would be greatly appreciated. I will summarize if anyone is interested. Thanks in advance, Steven E. Schafer S.U.N.Y. Binghamton Chemistry Department http://chemiris.chem.binghamton.edu:8080 Binghamton, New York USA From hyu@helios.genetics.com Mon Feb 27 17:53:24 1995 Received: from helios.genetics.com.helios.genetics.com for hyu@helios.genetics.com by www.ccl.net (8.6.9/930601.1506) id RAA13347; Mon, 27 Feb 1995 17:22:36 -0500 Received: by helios.genetics.com.helios.genetics.com (4.1/SMI-4.1) id AA15476; Mon, 27 Feb 95 17:22:24 EST Date: Mon, 27 Feb 1995 17:22:23 -0500 (EST) From: Hsiang-ai Yu Subject: DEC Alpha benchmark To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am looking for benchmark numbers for CHARMM on DEC 2100 server with the 21064A@275MHz chip. Does anyone know if they are available? I do have some numbers on DEC 3000 Model 500 with the 21064@150MHz chip, but would like to find out the relative performance to that of the 2100 server. Thanks. Best Regards, _______________________________________________________________________________ Hsiang-ai Yu Genetics Institute, Inc. | Phone: (617) 498-8905 SMDD | Fax: -8993 85 Bolton Street | E-mail: hyu@helios.genetics.com Cambridge, MA 02140 From garciae@ucsub.colorado.edu Mon Feb 27 21:53:25 1995 Received: from ucsub.colorado.edu for garciae@ucsub.colorado.edu by www.ccl.net (8.6.9/930601.1506) id VAA16498; Mon, 27 Feb 1995 21:16:41 -0500 Received: (from garciae@localhost) by ucsub.colorado.edu (8.6.10/8.6.9/CNS-3.5) id TAA29174; Mon, 27 Feb 1995 19:16:39 -0700 Date: Mon, 27 Feb 1995 19:16:38 -0700 (MST) From: Garcia Edgardo To: chemistry@ccl.net Subject: CCL: internal -> zyx summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, some time ago I posted the following questions to the list: 1. Does somebody know where I can get a code (C,C++,FORTRAN) that transforms internal mol. coordinates in x,y,z ? 2. A program (code) that gets a molecular file with charges and calculates the dipole. Thanks to all of you that helped with these questions. Edgardo Garcia Here is a summary. ------------------------------------------------------------------------------------ From lim@rani.chem.yale.eduMon Feb 13 10:04:43 1995 Date: Fri, 10 Feb 95 21:29:39 EST I can answer to the 2nd question. It's written in AWK but I guess you can convert it to whatever language. Here's a sample input of H2O: 8 0.000000 0.000000 0.127189 -0.330 1 0.000000 0.758094 -0.508756 0.165 1 0.000000 -0.758094 -0.508756 0.165 The first column is an atomic number, 2-4 th columns are (x,y,z) coord and the final column is an atomic charge. Cut out the following script, make it executable and name it 'dipole'. On the command line, you'd enter 'dipole inputfile'. >From the above example, you'll get a dipole moment of 1.007927 Debye. -Dongchul Lim --------------------- CUT HERE --------------------------------- #!/usr/bin/nawk -f BEGIN { number = "^[-+]?([0-9]+[.]?[0-9]*|[.][0-9]+)" \ "([eE][-+]?[0-9]+)?$" first = 1; natoms = 0; ANG_TO_DEBYE = 4.802813198; } !isdata($1,$2,$3,$4,$5) { if (!first) exit; first = 0; next; } { natoms++; an[natoms] = $1; x[natoms] = $2; y[natoms] = $3; z[natoms] = $4; charge[natoms] = $5; } END { if (natoms == 0) { printf("No atoms found.\n"); exit; } # calculate net charge and dipole moment netcharge = 0.0; dipx = dipy = dipz = 0.0; for(i=1;i<=natoms;i++) { dipx += charge[i] * (x[i] - x[1]); dipy += charge[i] * (y[i] - y[1]); dipz += charge[i] * (z[i] - z[1]); netcharge += charge[i]; } dipole = sqrt(dipx*dipx + dipy*dipy + dipz*dipz); # converts to debyes when distances are in angstroms dipole *= ANG_TO_DEBYE; printf("Net charge = % 10.6f\n", netcharge); printf("Dipole moment = % 10.6f Debye\n", dipole); } function isdata (s1, s2, s3, s4, s5) { if (match(s1, number) && match(s2, number) && match(s3, number) && match(s4, number) && match(s5, number)) return 1; else return 0; } --------------------- CUT HERE --------------------------------- >From : Suresh Singh Date: Mon, Feb 13, 1995 7:33 AM I got a piece of fortran code that transforms internal coordinates in the Z-format to cartesian coordinates. I can send you the the source code and demo input files. Since we operate through a firewall it is not possible for outsiders to access our machines. So, does any of your machines have an anymous ftp access? otherwise I will send it via e-mail. Let me know. From mrigank@imtech.ernet.in Mon Feb 27 09:47:34 1995 Date: Fri, 24 Feb 95 22:57:00 +0530 SUBROUTINE i2c C Converts Internal coordinates to cartesian coordinates. IMPLICIT NONE INTEGER MAT, MRS PARAMETER (MAT = 500, MRS = 20) INTEGER lo REAL rot(4,4), x(3,MAT), AM(MAT, 4, 4) REAL a, b, r INTEGER i, j, k, l, m, i1 C *** Molecular Topology C bl=bond length array <<<< C ba=bond angle array <<<<< C da= dihedral angle array <<<<< C natms= total number of atoms <<<<< C name=atom names array C con(4,..)= connectivity table. only con(1,i) is usefule here.<<<<< C chrg= partial atomic charge array C type= atomic type array C ngrup=total number of residues C grup=group(residue) numbers C resd=residue names C X(3,..) = cartesian coorinate array <<<<<< C ' <<<<<<' marked arrays are used here. rest are for compatibility with C other programs in MoMoS package and related stuff. C C Authors C DR. Mrigank Dr. V.Kothekar C Bioinformatics Centre Dept. of Biophysics C Institute of Microbial Technology All India Institute of Medical Sciences C Sector 39-A Ansari Nagar C Chandigarh 160 014 New Delhi 110 029 C mrigank@imtech.ernet.in[much preferred] koth@medinst.ernet.in, C mrigank@csimtech.ren.nic.in vkothek@aiims.ernet.in C tele: +91-172-690557 +91-11-6864851 C C This routine is part of MoMoS [MOlecular MOdelling and Simulation] package C -- -- - REAL bl(MAT), ba(MAT), da(MAT), chrg(MAT) INTEGER con(4,MAT), type(MAT), grup(MAT), natms, ngrp CHARACTER title*78, name(MAT)*4, resd(MRS)*4 COMMON + /mtr/ bl, ba, da, chrg + /mti/ con, type, grup, natms, ngrp + /mtc/ title, name, resd COMMON + /crt/ x IF(natms.EQ.0) THEN C RETURN END IF DO 10 i = 1, natms R=bl(i) A=0.017453*ba(i) B=0.017453*da(i) ROT(1,1)=-COS(A) ROT(1,2)=-SIN(A) ROT(1,3)=0.0 ROT(1,4) = -R*COS(A) ROT(2,1)= SIN(A)*COS(B) ROT(2,2)=-COS(A)*COS(B) ROT(2,3)=-SIN(B) ROT(2,4)=R*SIN(A)*COS(B) ROT(3,1)=SIN(A)*SIN(B) ROT(3,2)=-COS(A)*SIN(B) ROT(3,3)=COS(B) ROT(3,4)=R*SIN(A)*SIN(B) ROT(4,1)=0.0 ROT(4,2)=0.0 ROT(4,3)=0.0 ROT(4,4)=1.0 I1=con(1,i) DO 70 L=1,4 DO 70 M=1,4 AM(i,L,M)=0.0 IF(i.GT.1)GO TO 30 AM(i,L,M)=ROT(L,M) GO TO 70 30 DO 60 K=1,4 AM(i,L,M)= AM(i,L,M)+AM(i1,L,K)*ROT(K,M) 60 CONTINUE 70 CONTINUE DO 90 J=1,3 X(j,i)=AM(i,J,4) 90 CONTINUE 10 CONTINUE 3 CONTINUE c DO i = 1, natms c WRITE(lo, '(A4, 3F10.5, 4I4, 2X, F8.3, 2I2)') c + name(i), (x(j,i), j = 1, 3), (con(j,i), j = 1,4), chrg(i), c + name(i), x(1,i), x(2,i), x(3,i), (con(j,i), j = 1,4), c + chrg(i), type(i), grup(i) c END DO 5000 RETURN 2004 FORMAT(2A2,3F10.5,4I4,F10.3,2I2) END From pat@mercury.aichem.arizona.eduMon Feb 13 10:04:49 1995 Date: Fri, 10 Feb 1995 22:12:23 -0700 (MST) Our program Babel can do this. Info attached. Pat BABEL is a program designed to interconvert a number of file formats currently used in molecular modeling. The program is available for Unix (AIX, Ultrix, Sun-OS, Convex, SGI, Cray, Linux), MS-DOS, and on Macs running at least System 7.0. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file. INSTALLATION OVERVIEW Babel is availiable via anonymous ftp from joplin.biosci.arizona.edu in pub/Babel UNIX The Unix version is in the file babel-1.04.tar.Z 1. uncompress babel-1.0X.tar.Z 2. tar -xvf babel-1.0X.tar 3. follow the instructions in README.1ST -------Special note for users with Sun workstations------------------- Many older Sun C compilers are not ANSI compliant and will not compile Babel. However, there are two options : 1. Use gcc 2. Download the file sun-babel-1.0X.tar.Z which has a binary compiled with with gcc on a sun 4 under SunOS release 4.1.3. -------Special note for users with SGI workstations----------------------- It seems that some people who have SGI workstations don't have a C compiler. For these people we have put an SGI binary in the file sgi-babel-1.0X.tar.Z MAC The Mac version is in the file macbabel-1.03.sea.hqx 1. Use you favorite archiving program to unbinhex the archive. 2. Double click on the self extracting archive macbabel.sea 3. Follow the instructions in the file Babel Manual DOS The DOS version is in the file babel104.zip 1. pkunzip babel104.zip 2. follow the instructions in README.1ST Any questions regarding BABEL should be directed to babel@mercury.aichem.arizona.edu From Thomas.Bally@unifr.ch Mon Feb 13 10:04:56 1995 Date: Sat, 11 Feb 1995 10:44:10 +0100 Dear Edgardo, nearly every quantum chemical program contains code which does exactly what you require. As you can get the source of many of these codes, simply extract the portion(s) which do(es) what you require (i.e. the part which reads the Z-matrix input and the one which converts this into cartesians). It is probably easiest to try MOPAC or so, these tend to be more transparent than the ab-intio packages such as Gaussian. From hinsenk@ERE.UMontreal.CA Mon Feb 13 10:05:06 1995 Date: Sat, 11 Feb 95 09:23:04 -0500 I have recently written such a program in C++. It takes input files like --------------------------------------------------------------------------- molecule acetone act # Acetone geometry from # T. Ijima, Bull. Chem. Soc. Japan 45, 3526 (1972) # # H11 O H31 # \ || / # H12-C1--C2--C3-H32 c c2 0 0 0 # / \ # H13 H33 # Fix the C's and the O b c2 o 1.210 b c1 c2 1.517 b c2 c3 1.517 a c1 c2 c3 116 a c1 c2 o 122 d c1 c2 o c3 180 # Left methyl group; change dihedral to rotate d h11 c1 c2 c3 180 t c1 h11 h12 h13 x1 1.091 108.5 a x1 c1 c2 180 # Right methyl group; change dihedral to rotate d h31 c3 c2 c1 180 t c3 h31 h32 h33 x3 1.091 108.5 a x3 c3 c2 180 calculate translate cm end --------------------------------------------------------------------------- or Z-matrix style input such as --------------------------------------------------------------------------- molecule chloroform clf z C z H C 1.1 z CL1 C 1.758 H 107.57 z CL2 C 1.758 H 107.57 CL1 120.0 z CL3 C 1.758 H 107.57 CL1 -120.0 calculate translate cm end --------------------------------------------------------------------------- Once a molecule is defined, you can print its Cartesian coordinates or arbitrary internal coordinates. The program can also produce a PDB file for a molecule or an arbitrary configuration of molecules. The code is still relatively new and has therefore not yet been tested extensively. And of course it comes with no guarantee... I have checked it with g++ 2.6.3 and the Cfront-based compiler supplied by Silicon Graphics. Let me know if you are interested. From jstewart@fujitsu.com Mon Feb 13 10:05:13 1995 Date: Sat, 11 Feb 95 12:35:19 PST Please look in MOPAC 3 to MOPAC 7. The routines XYZINT go from Cartesian to internal, and GMETRY goes from internal to Cartesian. The routine DIPOLE calculates the dipole. Jimmy Stewart From ch11mh@surrey.ac.uk Mon Feb 13 10:05:25 1995 Date: Mon, 13 Feb 1995 00:12:03 +0000 (GMT) For xyz: Try Babel For dipoles : MOPAC will do this for you, except I think it will tend to calculate charges at the same time. It's a big program - read the manual. I think you should be able to get both these programs via anonymous FTP >from www.ccl.net in /pub/chemistry. BABEL and MOPAC run under DOS and UNIX. (MOPAC runs on OS/2 as well) From lim@rani.chem.yale.edu Mon Feb 27 23:59:10 1995 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by www.ccl.net (8.6.9/930601.1506) id XAA17904; Mon, 27 Feb 1995 23:20:17 -0500 Received: by rani.chem.yale.edu; Mon, 27 Feb 95 23:20:12 -0500 From: Dongchul Lim Message-Id: <9502280420.AA18868@rani.chem.yale.edu> Subject: conformational isomers To: chemistry@ccl.net (Computational Chemistry) Date: Mon, 27 Feb 95 23:20:12 EST X-Mailer: ELM [version 2.3 PL11] Here's a summary of the articles posted on the CCL and I received personally. I thank all who replied to my question. I chopped off signatures severely to save space. I hope you don't mind. --- original posting --- Is there a simple way of testing if two given conformational isomers are equivalent? E.g., how can you know the gauche (+) conformer of n-butane is equivalent to the gauche (-) conformer? My idea is 1) superimpose the two conformers. 2) if they are not superimposed, superimpose the one conformer and the mirror image of the other. __________________________________________________________________________ >From jordi@stark.udg.es Tue Feb 21 07:26:38 1995 There is a simple way of testing if two conformers are equivalent. You can know it just calculating the corresponding molecular self-similarity measures (MSM). Two equivalent conformers will have the same electronic density distribution, thus, their MSM value will be the same. Since calculation of the exact MSM value is not computationally feasible for large molecules, here you have some recent references on several approximations to evaluate the MSM for large systems: * J.Comp.Chem. 1994, 15, 1113-1120 * J.Am.Chem.Soc. 1994, 116, 5909-5915 * J.Chem.Inf.Comp.Sci. 1994, 34, 1047-1053 * Scientia gerundensis 1995, 21, xxx (in press) __________________________________________________________________________ >From MARTIN@cmda.abbott.com Tue Feb 21 09:07:35 1995 An easier way is to calculate the interatomic distances since that is invariant to reflection. We consider 0.3A tolerance to be the cut-off if two conformers are different. __________________________________________________________________________ >From Karl.F.Moschner@urlus.sprint.com Tue Feb 21 10:37:02 1995 Sounds about right to me, but, if your program doesn't do so already, you should first provide a "standard" orientation such as placing the origin at the center of mass and orienting the molecule along the principal moment axes or dipoles, if you include charges. But, depending on your code, you may still have to consider reversed orientation, i.e., check if x1(a) = x1(b) or x1(a) = -x1(b), if the latter, reverse the orientation, ditto for y and z. Besides exact superposition, quick screens are the total energy, dipole (if you include charges), and moments. For larger molecules, end-to-end or selected interatomic distances afford quick checks. And, if you're checking a series of molecules, molecular weight or elemental composition are effective screens. It's suprising that some/many molecular mechanics packages do not support/generate "standard" orientations since it would be helpful not only for your problem but also as a start for CoMFA alignments. However, you could easily write your own starting from MOPAC or GAMESS subroutines, if you have them. There may also be a program/subroutine available from QCPE which you could modify. A few years ago I had modified the GAMESS subroutine for determining the principal moments to generate standard orienetations for Tripos "*.mol" files. It was very fast, requiring only a several seconds to reorient lysozyme on an SGI 4D/35. Unfortunately I no longer have the code and would be prohibited from redistributing it even if I did. My original interest was to subsequently compute the 3 principal cross-sectional areas, and/or solvent cross-sectioanl areas, to try to relate them to diffusivities but I didn't get that far. __________________________________________________________________________ >From polowin@hyper.hyper.com Tue Feb 21 09:17:43 1995 Depends on what you mean by "equivalent", and how you're doing the superimposition. In molecular modelling, for example, even structures with the "same" conformation can differ significantly as a result of a slight shift in a torsional angle near the middle of a large system. If you were checking for "equivalence" by something like RMS deviation of atomic positions, you'd take them to be completely different. If you were checking bond angles and torsional angles, they'd probably appear to be pretty similar. __________________________________________________________________________ >From hendrick@agouron.com Tue Feb 21 12:26:39 1995 Hi The way this was done in MacroModel was to identify equilavent atoms and then check for identical conformers by doing rms superimposition with the equilivalent atoms. For example in your n-butane case (C1-C2-C3-C4), if you made atom one equivalent to atom four, and atom two equivalent to atom three and then do the rms superpositions, you would find the redundant conformers. Tom Hendrickson __________________________________________________________________________ From: lnl@novo.dk (Leif Norskov) > Is there a simple way of testing if two given conformational isomers > are equivalent? > E.g., how can you know the gauche (+) conformer of n-butane is > equivalent to the gauche (-) conformer? > My idea is [ to superimpose the conformers ]... If speed is a problem (and it could well be - consider for example the matching of the protons in butane) then it might be advantageous to first compare the moments of inertia, which of course are invariant to atom labelling and rotation/translation, before proceeding with superpositioning. __________________________________________________________________________ From: "E. Lewars" Dongchul Lim asked how one can tell if two conformers are the same. This is a special case of how to tell if two isomers are really the same species. It seems to me a simple approach is (after looking to see that they are not obviously different) to have your program (MOPAC, GAUSSIAN etc) calculate the total internuclear repulsions. Two species that look the same and have the same internuclear repulsions (to 6 or more decimals--Hartrees) are, I would think, extremely unlikely not to be the same. Many comp. chem programs calculate internucl. repulsions; if a check job wn't give that number, then ask for a single-point calc. using a fast method like a semiempirical routine. The actual internuclear repulsin calc. is trivial. Errol Lewars __________________________________________________________________________ From: peon@medchem.dfh.dk (Per-Ola Norrby) Your proposal is of course the only final test, but there are some ways to do a quick screening to avoid having to test a lot of conformations by superimposition. If your structures are output from some calculation, several commonly calculated criteria have to be equal for the two conformers. Two simple ones are calculated energy (only if you have fair convergence) and moment of inertia (very sensitive to conformational changes). You only need to superimpose structures that differ "very little" in these two test. __________________________________________________________________________ From: (sandeep kumar) I think one way to test the conformational equivalence esp. for small structures like n-butane is to calculate or measure the energies of the two isomers. For example, in case of n-butane both g+ and g- have almost equal energies i.e. both of them are almost equally stable while trans isomer has lower energy than any of the two and is much more stable than any of the two. I restrict myself to recomend its usage with small organic molecules with simple geometries only. for further disscussion on the matter please refer to organic chemistry text book by Morrison and Boyd. yours' cordially sandeep kumar san@mbu.iisc.ernet.in P.S. I shall be grateful to you if you summarize what you find. __________________________________________________________________________ From: Garcia Edgardo About the conf. isomers question of Dongchul Lim, my opinion is that first we should ask if we want to compare IDENTICAL or EQUIVALENT isomers (concerning energy for example). In the first case a simple superpossition will probably work. In the second we can make a non-bonding energy calculation and compare the energies or compare the distance matrix of the structures (or some kind of invariant of them) within some allowed range of values. __________________________________________________________________________ From: polowin@hyper.hyper.com (Joel Polowin) > From: "E. Lewars" > Subject: CCL:TELLING IF TWO CONFORMERS ARE IDENTICAL > > Dongchul Lim asked how one can tell if two conformers are the same. This is > a special case of how to tell if two isomers are really the same species. > It seems to me a simple approach is (after looking to see that they are > not obviously different) to have your program (MOPAC, GAUSSIAN etc) > calculate the total internuclear repulsions. Two species that look the same > and have the same internuclear repulsions (to 6 or more decimals--Hartrees) > are, I would think, extremely unlikely not to be the same. Many comp. > chem programs calculate internucl. repulsions; if a check job wn't give > that number, then ask for a single-point calc. using a fast method like > a semiempirical routine. The actual internuclear repulsin calc. is > trivial. I don't think the situation is quite so simple -- possibly depending on what is meant by conformers being "the same". If I have a large structure and alter a torsional angle in the middle by a fraction of a degree, it's probably still "the same structure". If the structure was energy- optimized before, it's very likely that trying to optimize it again won't do much to change it back unless there are other steric effects. But the atoms at the ends of this large structure will probably move a *lot* as the result of that tiny bend in the middle, and the internuclear repulsions are likely to change significantly too. Maybe only a little, or maybe some other local minimum would be found, but I don't think the internuclear repulsions would likely be the same to 6 or more decimals. I think that the matter depends critically on: What sort of structures are you trying to compare, and what do you mean by "the same"? Regards, Joel __________________________________________________________________________ From: valery-g@dcl.co.il (Dr. Golender Valery) Dear Lim, You asked on CCL how one can tell if two conformers are the same. I already saw some responses on the net advising to solve the problem from the molecular modeling point of view. In fact, there exist a strict mathematical formulation of this problem called isomorphism of 3D objects. It is a common problem arising in a number of applications including 3D database search, ligand design, spanning of conformational space and etc. A number of different algorithms and programs were proposed to solve this problem. Simple superposition suggested in the original posting is not working because of molecular symmetry. We recently developed an efficient algorithm incorporated into the conformer clustering utility of Apex-3D activity prediction system marketed by Biosym. I can provide more detailed information if you are interested in this functionality. __________________________________________________________________________ From: Karl.F.Moschner@urlus.sprint.com Sounds about right to me, but, if your program doesn't do so already, you should first provide a "standard" orientation such as placing the origin at the center of mass and orienting the molecule along the principal moment axes or dipoles, if you include charges. But, depending on your code, you may still have to consider reversed orientation, i.e., check if x1(a) = x1(b) or x1(a) = -x1(b), if the latter, reverse the orientation, ditto for y and z. Besides exact superposition, quick screens are the total energy, dipole (if you include charges), and moments. For larger molecules, end-to-end or selected interatomic distances afford quick checks. And, if you're checking a series of molecules, molecular weight or elemental composition are effective screens. It's suprising that some/many molecular mechanics packages do not support/generate "standard" orientations since it would be helpful not only for your problem but also as a start for CoMFA alignments. However, you could easily write your own starting from MOPAC or GAMESS subroutines, if you have them. There may also be a program/subroutine available from QCPE which you could modify. A few years ago I had modified the GAMESS subroutine for determining the principal moments to generate standard orienetations for Tripos "*.mol" files. It was very fast, requiring only a several seconds to reorient lysozyme on an SGI 4D/35. Unfortunately I no longer have the code and would be prohibited from redistributing it even if I did. My original interest was to subsequently compute the 3 principal cross-sectional areas, and/or solvent cross-sectioanl areas, to try to relate them to diffusivities but I didn't get that far. Good luck! __________________________________________________________________________ From: Mick Kappler > Is there a simple way of testing if two given conformational isomers > are equivalent? Yes. The Stereochemical Extended Morgan Algorithm (SEMA) developed by Wipke and Dyott provides a stereochemical canonical name. Comparison of the structure SEMA names is straight forward. __________________________________________________________________________ From: marvin@biosym.com (Marvin Waldman) > Is there a simple way of testing if two given conformational isomers > are equivalent? This is, in fact, quite a difficult and subtle question. The SEMA algorithm which Mick Sappler proposed can be used to detect if two CONFIGURATIONAL isomers are equivalent (ie. they have the same or different stereochemistry). However, it will not detect if the same configurational isomers are equivalent or not in a CONFORMATIONAL sense. SEMA cannot detect the difference between the gauche and trans forms of n-butane. These are CONFORMATIONAL isomers. The issue of the equivalence of two conformations is further complicated by the problem of topological symmetry. This makes an RMS comparison of atoms problematic for detecting equivalent conformations. For example, if I do an RMS comparison of corresponding atoms between two conformers in which the hydrogens of a methyl group are rotated by 120 degrees, I will detect an RMS difference because I am now comparing the wrong set of atoms. One needs to compare all combinations of topologically equivalent atoms in the molecule to see if they have a (virtually) zero RMS. If one proposes to do an RMS comparison of heavy atoms only, then you only need to replace the methyl group with a t-butyl group, and the problem remains. If one proposes to compare only energies (and not RMS), then, of course, the symmetry will be correctly handled for the energy, and you only need to worry about the somewhat unlikely case of two different conformers having (almost?) the same energy. Since these conformers are likely to come from some energy optimization procedure, roundoff error and tolerances used for the minimization implies that one needs to use some kind of tolerance in comparing energies, which always leads to the (remote?) possibility that nearly equal energies may not correspond to the same conformer. The larger the molecule and the more conformational flexibility (and therefore conformers) it has, the more likely that this somewhat theoretical problem may manifest itself in a real example. The ideal/correct solution would be to compare both the energy as well as all combinations of RMS comparisons of topologically equivalent atoms until the RMS difference found for a given comparison pair fell below some threshold. I am not aware of a software package that has actually implemented such an algorithm, and would be very interested to hear about one that does. So, the bottom line answer to the question, is: No, I don't think there is a SIMPLE way to do this. __________________________________________________________________________ From: "E. Lewars" When I suggested using the internuclear repulsion E to check if two isomers are identical, I should have pointed out that enantiomers have precisely the same energies--internuclear, electronic, etc (in the absence of a chiral perturbation; physicists may quibbl, too, that the negation of parity by the weak nuclear force causes a miniscule difference in enantiomer E's). Joel Polowin of HyperChem pointed out that as a practical matter identity isn't an all-or-nothing phenomenon: how similar do two species have to be for a chemist to call them the same thing? As several people said, there are sophisticated algorithms for matching up two molecules and looking at, e.g., RMS differences in geometric parameters. I think the widely- used MM program PCModel can do something like this; one or two other programs were mentioned. Joel's idea about a small tweak in one part of a molecule causing a ratcheting effect that's amplified elsewhere (cf. allosteric effects in enzymes?) is interesting. Errol Lewars =============================== Regarding internucl rep.--one could calc it for some test cases, alter these geometries slightly, and see if it might be useful for the problem at hand. =============== __________________________________________________________________________ From: "CBAS25 ::P_BLADON ::CBAS25" Dear Dongchul Lim, With regard to the conparisons of conformers. There are several points to consider. (1) If the problem involves small molecules like butane where the number of stable conformers is known, then simply superimposing the "unknown" structure on each of the "known" conformers in turn will give an answer. The rms deviation of atom positions or some other figure of merit will afford an answer even when an exact match is not achieved. (2) If the structures are more complex, perhaps involving large membered rings, then the number of conformers could be large. But suppose that you have a set of such structures, and wish to test which of them your "unknown" most resembles. You would still get an answer. If the "unknown" were a crystal structure and the "knowns" derived >from a conformer generating program, you would not expect a good match necessarily. What you could do then is to take the pair of best matched structures and refine them with your favourite MM or MO package, and see if they both decend into the same energy well. (3) To do the matching you could use atom to atom matching, or alternatively use the icosahedral matching algorithm in programs like COMPARISONS or CORRELATE. The first of these programs will match an "unknown" against a series of "unknowns", while the second would allow the correlation of a whole series of conformers. The matching of mirror-image forms is taken care of. Both programs are available from QCPE as part of the INTERCHEM package. __________________________________________________________________________ From: "Victor M. Rosas Garcia" Some people have mentioned algorithms for comparison of conformers and evidently the solution to this problem is far from simple. The best implementation I have seen to solve this problem is in the program GMMX, a global minimum search utility by Serena Software. As I understand it, the program calculates the RMS of the conformers by using identical numbering in the atoms of both conformers and, if necessary, checks for planes of symmetry and for the so-called numerical isomers. The idea is that making the atoms distinguishable by numbering them will introduce artificial conformers that differ only in the numbering but that are really "the same" conformer e.g. a product of a rotation or reflection or some other symmetry operation. __________________________________________________________________________ From: graham@sentex.net (Graham Hurst) >> Is there a simple way of testing if two given conformational isomers >> are equivalent? [good stuff deleted] >The ideal/correct solution would be to >compare both the energy as well as all combinations of RMS comparisons >of topologically equivalent atoms until the RMS difference found >for a given comparison pair fell below some threshold. I am not >aware of a software package that has actually implemented such >an algorithm, and would be very interested to hear about one that >does. The Conformational Search module of the ChemPlus set of extensions for HyperChem uses energy and RMS compairisons of topologically equivalent atom pairings. I've been following this discussion with some interest. When I wrote the Conformational Search module of ChemPlus, I implemented the following tests to compare for equivalent conformations that might result from the search. The comparisons available are (in the order that the program can optionally execute them) are: 1. Changed chirality (R or S) of chiral centers with 4 bonded neighbours. (Chiral centers are determined by HyperChem.) 2. Energy (from HyperChem) within a user adjustable range. 3. Varied torsions within a user adjustable range. This test is turned off by default, since it doesn't handle topologically equivalent dihedral angles. 4. R.M.S. deviation for a least-squares overlay of atoms. As Marvin Waldman pointed out, one needs to compare with all topologically equivalent permutations of atom order and this option (discussed further below) is available in ChemPlus. A subset of atoms can also be specified for the comparision. I initially included an option for comparison of inertial moments (suggested earlier by Leif Norskov ) but I abandoned it because it seemed too sensitive a measure, with suitable tolerances varying widely with the number of atoms. If the option to use equivalent atoms in the RMS comparison is turned on, the program generates all equivalent atom order permutations. The algorithm I used for this is basically brute force, O(N!) at worst, but being able to compare element type and number of bonds for each topological "node" allows considerable trimming of the paths. Further trimming results from only considering a subset of atoms (eg. no hydrogens or only backbone atoms) so that permutations of ignored atoms are unnecessary (assuming equivalent sets are either all included or all excluded). >So, the bottom line answer to the question, is: No, I don't think >there is a SIMPLE way to do this. I agree! It took me about a month to puzzle out and implement an algorithm for generating equivalent atom orders! As Valery Golender pointed out, the conformational isomer problem is a specific instance of isomorphism of 3D objects. Cheers, Graham P.S. If you want more ChemPlus or HyperChem product info, please send email to info@hyper.com, not to me because I don't work there anymore. __________________________________________________________________________ From: Matt Stahl Greetings, The problem of duplicate conformer removal certainly is challenging, especially to anyone doing extensive conformational searches. The "easy" method of detection is to compare a unique identifier based on atomic coordinates. Shape descriptors such as the sum of interatomic distances, or the sum of all triangles in a molecule provide a single number to identify a conformation. In this sense, energy is also a "shape descriptor" because it is simply a function operated on a set of coordinates. As pointed out by Dr. Waldman, there is always the possibility of ambiguity when using this kind of descriptor. I have seen cases in larger bicyclo alkanes where very different conformations had the same mechanics energy to the 5th or 6th decimal place! There are several matters that must be addressed with regard to comparing conformations. Rms fitting may not be the best measure of similarity when comparing long acyclic chains because of the 'torque' effect. Torsional comparisons certainly have valid applications. In general, rms fits work well with the exception of the problems of automorphism and enantiomeric coordinates. Generating enantiomers is trivial. Simply multiply all of the x, y, or z coordinates by -1 to generate the mirror image. Automorphisms can be more of a problem. They can be discovered by connectivity matrix manipulations (see balasubramanian in j. chem. inf. comp. sci. may/june 1994). A much quicker approach is to effectively do an atom-by-atom max common substructure search using comparisons of atom types. Once the automorphisms are discovered they can be used in both torsional and rms comparisons. Pat Walters and i have written a program called Padre (Population Analysis and Duplicate REmoval) that will read multi-structure files, automatically generate the automorphisms (and enantiomers if desired), and do rms or torsional comparisons and identify duplicate conformers. It will also map rings onto each other and compare all possible overlays. Padre is FAR from completion, but the features currently implemented are solid. Please contact me directly if you are interested in this software. __________________________________________________________________________ From: Mick Kappler > Is there a simple way of testing if two given conformational isomers > are equiva lent? This question can be interpreted in two ways, as Joel Polowin indicated. On Wed, 22 Feb 95 10:29:54 -0500, Joel Polowin wrote: > I don't think the situation is quite so simple -- possibly depending on > what is meant by conformers being "the same". If one is interested in structural equivalency independent of conformation, the SEMA algorithm (JACS, 96, 4834, 1974) is a solution. If one is interested in structural equivalency dependent of conformation, the solution is more complex, as Marvin Waldman pointed out. On Wed, 22 Feb 1995 14:47:42 -0800, Marvin Waldman wrote: > This is, in fact, quite a difficult and subtle question. The SEMA > algorithm which Mick Sappler proposed can be used to detect if > two CONFIGURATIONAL isomers are equivalent (ie. they have the > same or different stereochemistry). However, it will not detect > if the same configurational isomers are equivalent or not in > a CONFORMATIONAL sense. SEMA cannot detect the difference between > the gauche and trans forms of n-butane. These are CONFORMATIONAL > isomers. This is correct. The ultimate solution to the structural equivalency dependent of conformation problem will depend on analytical features of the two structures only. On Thu, 23 Feb 1995 01:47:29 EST, CBAS25 ::P_BLADON ::CBAS25 wrote: > There are several points to consider. > > (1) If the problem involves small molecules like butane where the number > of stable conformers is known... We can not assume we have anything but the two conformations that we wish to compare. Given a hypothetical structure, who knows the set of stable conformers? > (2) If the structures are more complex... then the number of conformers > could be large. But suppose that you have a set of such structures... Again, let's not assume we know. > (3) To do the matching you could use atom to atom matching... This could take a long time, considering the size of the set of structures to compare. Is time an issue? I imagine it is if you have a large set of structures to compare. On Wed, 22 Feb 1995 23:36:21 -0800, Victor M. Rosas Garcia wrote: > ...The best implementation I have seen to solve this problem is in the > program GMMX, a global minimum search utility by Serena Software. If this works for you, this is great. Unfortunately, this technique is only as good as the software and comparison of conformation A by software X to conformation B by software Y is impossible. Hence, comparisons between research groups may be a problem. This is not to mention the multiple minima problem, as E. Lewars pointed out. On Wed, 22 Feb 1995 17:10:28 -0500, E. Lewars wrote: > ...enantiomers have precisely the same energies... On Wed, 22 Feb 1995 23:32:59 -0500, Graham Hurst wrote: > The Conformational Search module of the ChemPlus set of extensions > for HyperChem uses energy and RMS compairisons of topologically > equivalent atom pairings. RMS comparisons look promising at first. Unfortunately, before the comparison can be made, the conformations need to be superimposed, which is independent of the conformation itself. Although the superimposition can be solved analytically, it is sometimes solved iteratively, and can be a source of contention. Can we solve this problem indepedent of transformation? I would love to hear more from experts in this field. This is an interesting problem and this discussion has increased our interest in publishing our latest work relating to conformational comparisons. __________________________________________________________________________ From: Ramesh Gopalaswamy I have been working with steroid conformational analysis in connection with receptor modeling. I have generated several (typically 100) structures (conformers) for each steroid using DGEOM program. Now I need to pick out those conformers that are unique. (DGEOM generated structures might converge to same minimum upon minimization). Any ideas on how to do that using commercial modeling software or other shareware programs? Also, how to run minimizations (for 100 or so structures) as a background job, instead of having to read in each structure on to the graphics interface? I have access to Quanta, Cerius2 and Sybyl. Thanks a lot. Ramesh (rameshg@umich.edu) __________________________________________________________________________ From: Harold Helson Hi DC, I hope you are well! If I remember Wipke & Dyott's paper on SEMA ("Stereochemically extended Morgan algorithm") correctly, they propose some modifications to treat conformers. Here is an idea that's not too carefully thought out, and would take more time than you probably want to invest, but -- hell, it's an interesting problem. Canonicalization algorithms, which deliver a unique description of a molecule, incorporate some representation of a given bond's environment. In topological algorithms, this may merely be the bond order. In con- figurational algorithms, it is more complex, also including cis/trans and chiral parity information. What you would do is append additional configurational information, such as dihedral relationships along the path being grown. This might be all there is to this problem. So you would perform conventional canonicalization, using the more detailed bonding representation. You end up with one or more paths of equal priority, the presence of more than one reflecting automor- phisms (symmetry). The power in SEMA is that it is a trivial operation to enumerate all the enantiomers and geometric isomers. I expect that you would similarly be able to trivially enu- merate all the conformations, provided (and it's a big proviso) that you limited the dihedral angles to, say, multiples of thirty degrees, or whatever number is small enough to be a good approximation, but large enough so that the number of possible conformations does not go rapidly to infinity. This is certainly a valid approximation in the gauche butane example you cite. You would be able to tell a mirror image because its stereochemical parity table (see Wipke & Dyott) would contain an inversion, but the extra, appended conformational table would be the same for both structures. You could tell configurational isomers because their stereochemical tables would be identical, but their conformational tables would differ. __________________________________________________________________________