From ragno@siros.caspur.it Tue Dec 12 06:13:08 1995 Received: from siros.caspur.it for ragno@siros.caspur.it by www.ccl.net (8.6.10/950822.1) id GAA08970; Tue, 12 Dec 1995 06:10:51 -0500 Received: by siros.caspur.it; id AA27604; Tue, 12 Dec 1995 11:50:14 +0100 Date: Tue, 12 Dec 1995 11:50:14 +0100 From: Rino Ragno Message-Id: <9512121050.AA27604@siros.caspur.it> To: chemistry@www.ccl.net Subject: docking compare? Hi netters, do someone of you know if it is possible to compare the energies obtained from the docking (inside sybyl) of the same complex but were the ligand has been placed in a opposite orientation? Any replay will be appreciated. thanks to all Rino RAGNO University of ROME Italy From ragno@siros.caspur.it Tue Dec 12 06:28:08 1995 Received: from siros.caspur.it for ragno@siros.caspur.it by www.ccl.net (8.6.10/950822.1) id GAA09020; Tue, 12 Dec 1995 06:15:44 -0500 Received: by siros.caspur.it; id AA27743; Tue, 12 Dec 1995 12:10:35 +0100 Date: Tue, 12 Dec 1995 12:10:35 +0100 From: Rino Ragno Message-Id: <9512121110.AA27743@siros.caspur.it> To: chemistry@www.ccl.net Subject: docking compare? Hi netters, do someone of you know if it is possible to compare the energies obtained from the docking (inside sybyl) of the same complex but were the ligand has been placed in a opposite orientation? Any replay will be appreciated. thanks to all Rino RAGNO University of ROME Italy From ragno@siros.caspur.it Tue Dec 12 06:42:19 1995 Received: from siros.caspur.it for ragno@siros.caspur.it by www.ccl.net (8.6.10/950822.1) id FAA08744; Tue, 12 Dec 1995 05:54:35 -0500 Received: by siros.caspur.it; id AA27604; Tue, 12 Dec 1995 11:50:14 +0100 Date: Tue, 12 Dec 1995 11:50:14 +0100 From: Rino Ragno Message-Id: <9512121050.AA27604@siros.caspur.it> To: chemistry@www.ccl.net Subject: docking compare? Hi netters, do someone of you know if it is possible to compare the energies obtained from the docking (inside sybyl) of the same complex but were the ligand has been placed in a opposite orientation? Any replay will be appreciated. thanks to all Rino RAGNO University of ROME Italy From ccl@cric.chemres.hu Tue Dec 12 07:13:08 1995 Received: from cric.chemres.hu for ccl@cric.chemres.hu by www.ccl.net (8.6.10/950822.1) id HAA09459; Tue, 12 Dec 1995 07:03:57 -0500 From: Received: by cric.chemres.hu (AIX 3.2/UCB 5.64/4.03) id AA12878; Tue, 12 Dec 1995 13:00:51 +0100 Date: Tue, 12 Dec 1995 13:00:51 +0100 (NFT) To: TOPPER ROBERT Cc: chemistry@www.ccl.net, topper@cooper.edu Subject: Re: CCL:Units Conversion In-Reply-To: <199512111720.AA25274@zeus.cooper.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII As far as I know 1 Angstrom IS exactly 10^-10 m. The crystallographic unit (X untit) deviates from it because in the old time people used to determine the actual value of an Angstrom using some (cesium-oxid?) crystall of known crystallographyc structure, known density, the Avogadro number etc. Then the density was corrected, so all data obtained through the callibration mentioned, which were given in "Angstroms", need a slight correction. Ceterum censeo: 1 Angstrom = 10^-10 m, EXACTLY. Regards, I.M. From owner-chemistry@ccl.net Tue Dec 12 08:43:10 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id IAA10372; Tue, 12 Dec 1995 08:37:32 -0500 Received: from harfang.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by bedrock.ccl.net (8.7.1/950822.1) id IAA29931; Tue, 12 Dec 1995 08:37:29 -0500 (EST) Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id IAA15761 (8.6.11/IDA-1.6); Tue, 12 Dec 1995 08:36:52 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id IAA01370; Tue, 12 Dec 1995 08:36:52 -0500 Received: by cyclone.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id IAA08405; Tue, 12 Dec 1995 08:36:51 -0500 Date: Tue, 12 Dec 1995 08:36:51 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <199512121336.IAA08405@cyclone.ERE.UMontreal.CA> To: frits@chemde4.leidenuniv.nl CC: chemistry@ccl.net In-reply-to: <9512111138.AA16614@chemde4.leidenuniv.nl> (frits@chemde4.leidenuniv.nl) Subject: Re: CCL:Re: CCL:MATRIX ALGEBRA PROGRAM That's what I did (including the library itself :-( reinventing the wheel) but I am NOT sorry, because it is very convenient to be able to work with matrices just from the UNIX shell (with these tools) instead of writing programs for each case: i.e. (imaginary UNIX session) do some calculations, obtain some numerical results, use a tiny self-written tool to extract data from e.g. GAMESS or G94 output, mat_mult > C mat_eigval > Ceigval look at the eigenvalues, continue work,... There are several high-level matrix languages designed for exactly this kind of use. The best known is probably Matlab and its many clones, some of which are free (e.g. the GNU-clone called octave). There are also a few such languages that improve on Matlab's most obvious limitation, namely that matrices can only be two-dimensional. Check http://lusk1.mines.edu/hjjou/linux_prg.html for a list (it claims to be for Linux, but most of these packages are available for all Unix systems). One problem with these matrix languages is that they neglect other aspects of programming, most notably flexible I/O and interfacing with other programs. It would be a pain to write Matlab code to extract something from a Gaussian output file, for example. Which is why my favourite for such operations is Python. Python is a high-level object-oriented language designed for scripting and rapid prototyping (see http://www.python.org for details), and the implementation works on all relevant platforms and is completely free (there's not even a GNU-style "copyleft"). It has all the features of a scripting language (easy string and file handling, regular expressions etc.), but is also easily extensible in C or C++. One such extension which is being worked on now is a matrix-handling facility that makes numerical computations very convenient. Howeve, it is not yet available to the general public; if you want to try it you have to join the Matrix-SIG (which costs you just an e-mail); see the Python home page for details. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From topper@cooper.edu Tue Dec 12 09:13:10 1995 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.6.10/950822.1) id JAA10727; Tue, 12 Dec 1995 09:04:16 -0500 Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA07777 (5.65c/IDA-1.4.4 for ); Tue, 12 Dec 1995 09:06:53 -0500 Received: by zeus.cooper.edu id AA26294 (5.67b/IDA-1.5); Tue, 12 Dec 1995 08:59:53 -0500 Date: Tue, 12 Dec 1995 08:59:53 -0500 From: TOPPER ROBERT Message-Id: <199512121359.AA26294@zeus.cooper.edu> To: ccl@cric.chemres.hu, topper@cooper.edu Subject: Re: CCL:Units Conversion Cc: chemistry@www.ccl.net Content-Length: 1653 > > As far as I know 1 Angstrom IS exactly 10^-10 m. The crystallographic unit > (X untit) deviates from it because in the old time people used to determine > the actual value of an Angstrom using some (cesium-oxid?) crystall of > known crystallographyc structure, known density, the Avogadro number etc. > Then the density was corrected, so all data obtained through the callibration > mentioned, which were given in "Angstroms", need a slight correction. > > Ceterum censeo: > > 1 Angstrom = 10^-10 m, EXACTLY. > > Regards, > > I.M. > Oh, absolutely. I guess, this being cyberspace, you couldn't see that my tongue was placed firmly in my cheek when I said that... the "crystallographic angstrom" is, for this reason, symbolized with an asterix (*) after the A. best, rqt ************************************************************************ Robert Q. Topper email: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 USA or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/depts_info/topper.html ************************************************************************ The Cooper Union for the Advancement of Science and Art, founded in 1859, is a private institution of higher learning where all students receive full-tuition scholarships to study engineering, architecture and art. ************************************************************************ From ragno@siros.caspur.it Tue Dec 12 10:58:11 1995 Received: from siros.caspur.it for ragno@siros.caspur.it by www.ccl.net (8.6.10/950822.1) id FAA08744; Tue, 12 Dec 1995 05:54:35 -0500 Received: by siros.caspur.it; id AA27604; Tue, 12 Dec 1995 11:50:14 +0100 Date: Tue, 12 Dec 1995 11:50:14 +0100 From: Rino Ragno Message-Id: <9512121050.AA27604@siros.caspur.it> To: chemistry@www.ccl.net Subject: docking compare? Hi netters, do someone of you know if it is possible to compare the energies obtained from the docking (inside sybyl) of the same complex but were the ligand has been placed in a opposite orientation? Any replay will be appreciated. thanks to all Rino RAGNO University of ROME Italy From ragno@siros.caspur.it Tue Dec 12 11:13:12 1995 Received: from siros.caspur.it for ragno@siros.caspur.it by www.ccl.net (8.6.10/950822.1) id GAA08970; Tue, 12 Dec 1995 06:10:51 -0500 Received: by siros.caspur.it; id AA27604; Tue, 12 Dec 1995 11:50:14 +0100 Date: Tue, 12 Dec 1995 11:50:14 +0100 From: Rino Ragno Message-Id: <9512121050.AA27604@siros.caspur.it> To: chemistry@www.ccl.net Subject: docking compare? Hi netters, do someone of you know if it is possible to compare the energies obtained from the docking (inside sybyl) of the same complex but were the ligand has been placed in a opposite orientation? Any replay will be appreciated. thanks to all Rino RAGNO University of ROME Italy From owner-chemistry@ccl.net Tue Dec 12 11:21:15 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id IAA10372; Tue, 12 Dec 1995 08:37:32 -0500 Received: from harfang.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by bedrock.ccl.net (8.7.1/950822.1) id IAA29931; Tue, 12 Dec 1995 08:37:29 -0500 (EST) Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id IAA15761 (8.6.11/IDA-1.6); Tue, 12 Dec 1995 08:36:52 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id IAA01370; Tue, 12 Dec 1995 08:36:52 -0500 Received: by cyclone.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id IAA08405; Tue, 12 Dec 1995 08:36:51 -0500 Date: Tue, 12 Dec 1995 08:36:51 -0500 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <199512121336.IAA08405@cyclone.ERE.UMontreal.CA> To: frits@chemde4.leidenuniv.nl CC: chemistry@ccl.net In-reply-to: <9512111138.AA16614@chemde4.leidenuniv.nl> (frits@chemde4.leidenuniv.nl) Subject: Re: CCL:Re: CCL:MATRIX ALGEBRA PROGRAM That's what I did (including the library itself :-( reinventing the wheel) but I am NOT sorry, because it is very convenient to be able to work with matrices just from the UNIX shell (with these tools) instead of writing programs for each case: i.e. (imaginary UNIX session) do some calculations, obtain some numerical results, use a tiny self-written tool to extract data from e.g. GAMESS or G94 output, mat_mult > C mat_eigval > Ceigval look at the eigenvalues, continue work,... There are several high-level matrix languages designed for exactly this kind of use. The best known is probably Matlab and its many clones, some of which are free (e.g. the GNU-clone called octave). There are also a few such languages that improve on Matlab's most obvious limitation, namely that matrices can only be two-dimensional. Check http://lusk1.mines.edu/hjjou/linux_prg.html for a list (it claims to be for Linux, but most of these packages are available for all Unix systems). One problem with these matrix languages is that they neglect other aspects of programming, most notably flexible I/O and interfacing with other programs. It would be a pain to write Matlab code to extract something from a Gaussian output file, for example. Which is why my favourite for such operations is Python. Python is a high-level object-oriented language designed for scripting and rapid prototyping (see http://www.python.org for details), and the implementation works on all relevant platforms and is completely free (there's not even a GNU-style "copyleft"). It has all the features of a scripting language (easy string and file handling, regular expressions etc.), but is also easily extensible in C or C++. One such extension which is being worked on now is a matrix-handling facility that makes numerical computations very convenient. Howeve, it is not yet available to the general public; if you want to try it you have to join the Matrix-SIG (which costs you just an e-mail); see the Python home page for details. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Dec 12 15:28:16 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id PAA18724; Tue, 12 Dec 1995 15:27:17 -0500 Received: from tnt.syr.edu for wtwinter@mailbox.syr.edu by bedrock.ccl.net (8.7.1/950822.1) id PAA05655; Tue, 12 Dec 1995 15:27:14 -0500 (EST) Received: from kong.syr.edu (128.230.1.200) by tnt.syr.edu (LSMTP for Windows NT v1.0a) with SMTP id 5FD60DA0 ; Tue, 12 Dec 1995 15:27:40 -0500 Received: by kong.syr.edu (4.1/Spike-2.0) id AA02094; Tue, 12 Dec 95 15:26:06 EST Date: Tue, 12 Dec 1995 15:26:05 -0500 (EST) From: "William T. Winter" X-Sender: wtwinter@kong.syr.edu To: Hinsen Konrad Cc: frits@chemde4.leidenuniv.nl, chemistry@ccl.net Subject: Re: CCL:G:MATRIX ALGEBRA PROGRAM In-Reply-To: <199512121336.IAA08405@cyclone.ERE.UMontreal.CA> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII For access to a huge collection of matrix algebra and other mathematical libraries point your web browser at http://www.netlib.org/liblist.html EISPACK, LAPACK, LINPACK etc etc its all here and downloadable through the web. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786 URL http://www-chem.esf.edu From IRIKURA@ENH.NIST.GOV Tue Dec 12 17:28:17 1995 Received: from ENH.NIST.GOV for IRIKURA@ENH.NIST.GOV by www.ccl.net (8.6.10/950822.1) id RAA20436; Tue, 12 Dec 1995 17:21:23 -0500 From: Received: from ENH.NIST.GOV by ENH.NIST.GOV (PMDF V5.0-5 #10952) id <01HYQ78P3RN400VTDB@ENH.NIST.GOV> for chemistry@www.ccl.net; Tue, 12 Dec 1995 17:18:32 -0500 (EST) Date: Tue, 12 Dec 1995 17:18:31 -0500 (EST) Subject: ACS Symposium -- Computational Thermochemistry To: chemistry@www.ccl.net Message-id: <01HYQ78P5WSY00VTDB@ENH.NIST.GOV> X-PS-Qualifiers: /LEFT_MARGIN=6/SIZE=11 X-VMS-To: IN%" chemistry@www.ccl.net" X-VMS-Cc: IRIKURA MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT -- Symposium announcement -- COMPUTATIONAL THERMOCHEMISTRY American Chemical Society COMP Division 212th National Meeting Orlando, Florida August 25-30, 1996 ...including any computer-based means for predicting the thermochemical properties of a substance. This encompasses everything from group methods to high-level ab initio calculations. Potential topic areas include: * Advances in Group Contribution Techniques * New Software to Predict Thermochemistry * New Computational Techniques * Validation of Predictive Methods * Applications of Techniques to Practical Problems In addition to the technical presentations, there will be a panel discussion of the needs for and applications of accurate thermochemical data. The panel is intended to represent the users of thermochemical data in areas such as chemical processing, microelectronics, atmospheric modeling, the military, etc. We are now trying to identify the best possible panel members and will appreciate any suggestions. So far, the following speakers have accepted invitations to the symposium: A. D. Becke (Queen's University); S. W. Benson (University of Southern California); J. W. Bozzelli (New Jersey Institute of Technology); C. J. Cramer/D. G. Truhlar (University of Minnesota); L. A. Curtiss (Argonne National Laboratory); D. A. Dixon (Pacific Northwest National Laboratory); E. S. Domalski (National Institute of Standards and Technology); R. S. Drago (University of Florida); K. Harrison (University of Southern Alabama); A. J. Holder (University of Missouri); T. J. Lee (NASA Ames Research Center); M. L. Mavrovouniotis (Northwestern University); C. F. Melius (Sandia National Laboratories); G. A. Petersson (Wesleyan University); P. Politzer (University of New Orleans); P. E. M. Siegbahn/M. R. A. Blomberg (University of Stockholm); T. Ziegler (The University of Calgary). If you wish to contribute an oral or poster paper, or if you would like to suggest speakers, panel members, etc., please contact one of the organizers (below). For planning purposes, we would appreciate receiving the titles of contributed papers before the Spring meeting. Dr. Karl K. Irikura Dr. David J. Frurip National Institute of Standards & Technology The Dow Chemical Company (301) 975-2510 (517) 636-2446 fax 301-926-4513 fax 517-638-6027 irikura @ enh.nist.gov dfrurip @ dow.com From chtdjs@lv.levels.unisa.edu.au Tue Dec 12 19:13:21 1995 Received: from bROLga.Levels.UniSA.Edu.Au for chtdjs@lv.levels.unisa.edu.au by www.ccl.net (8.6.10/950822.1) id TAA21812; Tue, 12 Dec 1995 19:10:18 -0500 Received: from IW19-12079.Levels.UniSA.Edu.Au ("port 1494"@IW19-12079.Levels.UniSA.Edu.Au) by Levels.UniSA.Edu.Au (PMDF V5.0-4 #9510) id <01HYR7XJBMQA9AMETD@Levels.UniSA.Edu.Au> for chemistry@www.ccl.net; Wed, 13 Dec 1995 10:40:06 +0930 Date: Wed, 13 Dec 1995 10:40:06 +0930 Date-warning: Date header was inserted by Levels.UniSA.Edu.Au From: chtdjs@lv.levels.unisa.edu.au (Darren Simpson) Subject: CM5 and SINDO1 X-Sender: chtdjs@lv.levels.unisa.edu.au To: chemistry@www.ccl.net Message-id: <01HYR7XJDRW49AMETD@Levels.UniSA.Edu.Au> MIME-version: 1.0 X-Mailer: Windows Eudora Version 1.4.3b4 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Hello CCL'ers, I am looking for a quantum mechanical program/software, suitable for a CM5 or MASPAR (UNIX?) and capable of running semi-empirical calculations on 1st row transition elements. Moreover, does anybody know of a program capable of SINDO1 calculations on 1st row transition elements? This software must be Windows, DOS or UNIX (for CM5/MASPAR) compatible. Any suggestions are appreciated. Many thanks, Darren Simpson University of South Australia From arthur@csb0.IPC.PKU.EDU.CN Tue Dec 12 21:43:20 1995 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id VAA22865; Tue, 12 Dec 1995 21:31:12 -0500 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA05707; Tue, 12 Dec 95 20:21:10 -0800 Date: Tue, 12 Dec 1995 20:21:09 -0800 (PST) From: Arthur Wang To: CCL mailing list Subject: Problem in reading PDB (Continued) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, everyone! Last week I posted the question about SYBYL's problem in reading PDB files. Till now, I have got more than a dozen of kind replies, including two from Tripos Inc. A thousand thanks for those who have offer their help. Now I would like continue the discussion. Almost every people who has replied pointed out that PDB is not the proper format for small molecules. Some information may lose when a molecule is saved in PDB format. But...Mm..., I have to do so at least at present. As for the test example of biphenly, I changed the substructure name from PHE to something else according to other's suggestion. And I found this trick worked. I could reread the molecule with C.ar were misrecognized as C.2, but without missing atoms any more. I also found why the PDB files generated by QUANTA could not be accepted by SYBYL. You must use the label "HETATM" rather than "ATOM" in the PDB file. Then SYBYL can read in the file with the correct connectivity. No atom is missing. But, the atom types are still a complete mess. SYBYL can not assign the right atom type to each atom. Very strange results, such as a hydrogen with three valences, might be reported. (QUANTA can not assign the right atom types to a molecule in PDB format either. But at least it can assign the right element type to each atom.) It is a tough job to modify every atom to its right type, isn't it? So, any idea? Someone has mentioned the program BABEL. What is it? What can it do? Where can I get it? Any hint is appreciated. I paste a PBD file to the tail of this mail. The symbols at the atom name column are the atom types in AMBER force field, which you can guess without problem. This PDB file serves as another test example. Who can solve it by SYBYL? I can not wait to see the answer. Best Wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ Arthur Wang Doctoral Candidate _/ _/ _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-2501490 Fax: 86-10-2501725 _/ _/ WWW: http://www.ipc.pku.edu.cn/arthur/home.html _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ (CUT HERE) ----------------------------------------------------------------------------- REMARK MOLECULE 4123 HETATM 1 C LIG 1 2.293 2.413 1.706 HETATM 2 C LIG 1 1.393 1.598 1.115 HETATM 3 C2 LIG 1 3.705 1.908 2.007 HETATM 4 C3 LIG 1 4.269 2.287 3.410 HETATM 5 NT LIG 1 1.945 3.649 2.006 HETATM 6 C LIG 1 0.004 1.989 0.814 HETATM 7 O LIG 1 -0.350 3.131 1.077 HETATM 8 OH LIG 1 -0.827 1.103 0.240 HETATM 9 C3 LIG 1 0.703 3.631 2.792 HETATM 10 CH LIG 1 3.014 4.282 2.792 HETATM 11 C LIG 1 4.055 4.899 1.839 HETATM 12 C2 LIG 1 2.413 5.387 3.680 HETATM 13 O LIG 1 3.905 4.810 0.632 HETATM 14 CA LIG 1 5.285 5.628 2.410 HETATM 15 CA LIG 1 7.522 6.954 3.449 HETATM 16 CA LIG 1 5.457 5.730 3.796 HETATM 17 CA LIG 1 6.231 6.189 1.544 HETATM 18 CA LIG 1 6.576 6.393 4.315 HETATM 19 CA LIG 1 7.350 6.852 2.064 HETATM 20 C3 LIG 1 2.979 6.160 3.968 HETATM 21 CH LIG 1 -1.196 1.724 -0.994 HETATM 22 C2 LIG 1 -1.398 0.643 -2.072 HETATM 23 C3 LIG 1 -2.507 2.509 -0.802 HETATM 24 NT LIG 1 -2.298 -0.400 -1.558 HETATM 25 H LIG 1 -1.948 -0.738 -0.650 HETATM 26 C2 LIG 1 -3.647 0.158 -1.387 HETATM 27 CA LIG 1 -4.673 -0.989 -1.327 HETATM 28 CA LIG 1 -6.539 -3.074 -1.219 HETATM 29 CA LIG 1 -4.341 -2.193 -0.694 HETATM 30 CA LIG 1 -5.938 -0.827 -1.906 HETATM 31 CA LIG 1 -5.274 -3.235 -0.640 HETATM 32 CA LIG 1 -6.871 -1.870 -1.852 CONECT 1 2 3 5 CONECT 2 1 6 CONECT 3 1 4 CONECT 4 3 CONECT 5 1 9 10 CONECT 6 2 7 8 CONECT 7 6 CONECT 8 6 21 CONECT 9 5 CONECT 10 5 11 12 CONECT 11 10 13 14 CONECT 12 10 20 CONECT 13 11 CONECT 14 11 16 17 CONECT 15 18 19 CONECT 16 14 18 CONECT 17 14 19 CONECT 18 15 16 CONECT 19 15 17 CONECT 20 12 CONECT 21 8 22 23 CONECT 22 21 24 CONECT 23 21 CONECT 24 22 25 26 CONECT 25 24 CONECT 26 24 27 CONECT 27 26 29 30 CONECT 28 31 32 CONECT 29 27 31 CONECT 30 27 32 CONECT 31 28 29 CONECT 32 28 30 END From owner-chemistry@ccl.net Tue Dec 12 22:13:21 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id WAA23466; Tue, 12 Dec 1995 22:03:12 -0500 Received: from inetnif.niftyserve.or.jp for JDA03546@niftyserve.or.jp by bedrock.ccl.net (8.7.1/950822.1) id WAA09412; Tue, 12 Dec 1995 22:03:08 -0500 (EST) Received: by inetnif.niftyserve.or.jp (8.6.9+2.4W/3.3W8-950117-Mail-Gateway) id MAA14933; Wed, 13 Dec 1995 12:04:11 +0900 Message-Id: <199512130304.MAA14933@inetnif.niftyserve.or.jp> Date: Wed, 13 Dec 1995 11:36:00 +0900 From: "JDA03546@niftyse" Subject: UHF v.s. ROHF To: chemistry@ccl.net Dear all, I'm calculating some open shell systems with gaussian 94. I've been using UHF but since my systems are suffering from the terrible spin contaminations, I'm considering to use ROHF. Anyway, I just tested with the simplest case, dissociated H2. I set the atomic distance 5A and calculated with both UHF and ROHF. The total energy and MO coeff. were equal. UHF: SCF Done: E(UHF) = -.933163683734 A.U. after 1 cycles Alpha Molecular Orbital Coefficients 1 2 (SGG)--O (SGU)--O EIGENVALUES -- -.46668 -.46648 1 1 H 1S .70707 .70714 2 2 H 1S .70707 -.70714 Beta Molecular Orbital Coefficients. 1 2 (SGG)--V (SGU)--V EIGENVALUES -- .30788 .30817 1 1 H 1S .70707 .70714 2 2 H 1S .70707 -.70714 ROHF: SCF Done: E(ROHF) = -.933163683734 A.U. after 1 cycles Molecular Orbital Coefficients 1 2 (SGG)--O (SGU)--O EIGENVALUES -- -.05293 -.05277 1 1 H 1S .70707 .70714 2 2 H 1S .70707 -.70714 Since this is dissociated, the electrons should be delocalized. To obtain this picture, I did natural orbital analysis. And here UHF and ROHF contradicts. UHF: Natural Orbital Coefficients 1 2 EIGENVALUES -- 1.00000 1.00000 1 1 H 1S .96171 -.27406 2 2 H 1S .27395 .96174 ROHF: Natural Orbital Coefficients 1 2 EIGENVALUES -- 1.00000 1.00000 1 1 H 1S .78213 -.62311 2 2 H 1S .62303 .78220 Now a question rises. What I understand is in ROHF alpha and beta electrons are restricted to occupy the same spacial orbitals. Then, shouldn't all the properties calculated from ROHF and from UHF be the same if alpha and beta orbitals are equal (and equal to the ROHF orbitals) as this case? What am I missing? ** JDA03546@niftyserve.or.jp/Kazuo Teraishi <12/13 11:32> ** From arthur@csb0.IPC.PKU.EDU.CN Tue Dec 12 23:58:22 1995 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id XAA23997; Tue, 12 Dec 1995 23:43:19 -0500 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA05707; Tue, 12 Dec 95 20:21:10 -0800 Date: Tue, 12 Dec 1995 20:21:09 -0800 (PST) From: Arthur Wang To: CCL mailing list Subject: Problem in reading PDB (Continued) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, everyone! Last week I posted the question about SYBYL's problem in reading PDB files. Till now, I have got more than a dozen of kind replies, including two from Tripos Inc. A thousand thanks for those who have offer their help. Now I would like continue the discussion. Almost every people who has replied pointed out that PDB is not the proper format for small molecules. Some information may lose when a molecule is saved in PDB format. But...Mm..., I have to do so at least at present. As for the test example of biphenly, I changed the substructure name from PHE to something else according to other's suggestion. And I found this trick worked. I could reread the molecule with C.ar were misrecognized as C.2, but without missing atoms any more. I also found why the PDB files generated by QUANTA could not be accepted by SYBYL. You must use the label "HETATM" rather than "ATOM" in the PDB file. Then SYBYL can read in the file with the correct connectivity. No atom is missing. But, the atom types are still a complete mess. SYBYL can not assign the right atom type to each atom. Very strange results, such as a hydrogen with three valences, might be reported. (QUANTA can not assign the right atom types to a molecule in PDB format either. But at least it can assign the right element type to each atom.) It is a tough job to modify every atom to its right type, isn't it? So, any idea? Someone has mentioned the program BABEL. What is it? What can it do? Where can I get it? Any hint is appreciated. I paste a PBD file to the tail of this mail. The symbols at the atom name column are the atom types in AMBER force field, which you can guess without problem. This PDB file serves as another test example. Who can solve it by SYBYL? I can not wait to see the answer. Best Wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ Arthur Wang Doctoral Candidate _/ _/ _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-2501490 Fax: 86-10-2501725 _/ _/ WWW: http://www.ipc.pku.edu.cn/arthur/home.html _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ (CUT HERE) ----------------------------------------------------------------------------- REMARK MOLECULE 4123 HETATM 1 C LIG 1 2.293 2.413 1.706 HETATM 2 C LIG 1 1.393 1.598 1.115 HETATM 3 C2 LIG 1 3.705 1.908 2.007 HETATM 4 C3 LIG 1 4.269 2.287 3.410 HETATM 5 NT LIG 1 1.945 3.649 2.006 HETATM 6 C LIG 1 0.004 1.989 0.814 HETATM 7 O LIG 1 -0.350 3.131 1.077 HETATM 8 OH LIG 1 -0.827 1.103 0.240 HETATM 9 C3 LIG 1 0.703 3.631 2.792 HETATM 10 CH LIG 1 3.014 4.282 2.792 HETATM 11 C LIG 1 4.055 4.899 1.839 HETATM 12 C2 LIG 1 2.413 5.387 3.680 HETATM 13 O LIG 1 3.905 4.810 0.632 HETATM 14 CA LIG 1 5.285 5.628 2.410 HETATM 15 CA LIG 1 7.522 6.954 3.449 HETATM 16 CA LIG 1 5.457 5.730 3.796 HETATM 17 CA LIG 1 6.231 6.189 1.544 HETATM 18 CA LIG 1 6.576 6.393 4.315 HETATM 19 CA LIG 1 7.350 6.852 2.064 HETATM 20 C3 LIG 1 2.979 6.160 3.968 HETATM 21 CH LIG 1 -1.196 1.724 -0.994 HETATM 22 C2 LIG 1 -1.398 0.643 -2.072 HETATM 23 C3 LIG 1 -2.507 2.509 -0.802 HETATM 24 NT LIG 1 -2.298 -0.400 -1.558 HETATM 25 H LIG 1 -1.948 -0.738 -0.650 HETATM 26 C2 LIG 1 -3.647 0.158 -1.387 HETATM 27 CA LIG 1 -4.673 -0.989 -1.327 HETATM 28 CA LIG 1 -6.539 -3.074 -1.219 HETATM 29 CA LIG 1 -4.341 -2.193 -0.694 HETATM 30 CA LIG 1 -5.938 -0.827 -1.906 HETATM 31 CA LIG 1 -5.274 -3.235 -0.640 HETATM 32 CA LIG 1 -6.871 -1.870 -1.852 CONECT 1 2 3 5 CONECT 2 1 6 CONECT 3 1 4 CONECT 4 3 CONECT 5 1 9 10 CONECT 6 2 7 8 CONECT 7 6 CONECT 8 6 21 CONECT 9 5 CONECT 10 5 11 12 CONECT 11 10 13 14 CONECT 12 10 20 CONECT 13 11 CONECT 14 11 16 17 CONECT 15 18 19 CONECT 16 14 18 CONECT 17 14 19 CONECT 18 15 16 CONECT 19 15 17 CONECT 20 12 CONECT 21 8 22 23 CONECT 22 21 24 CONECT 23 21 CONECT 24 22 25 26 CONECT 25 24 CONECT 26 24 27 CONECT 27 26 29 30 CONECT 28 31 32 CONECT 29 27 31 CONECT 30 27 32 CONECT 31 28 29 CONECT 32 28 30 END