From chemistry-request@server.ccl.net Mon Jul 29 05:23:42 2002 Received: from web12801.mail.yahoo.com ([216.136.174.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6T9Nff23174 for ; Mon, 29 Jul 2002 05:23:41 -0400 Message-ID: <20020729092341.90980.qmail@web12801.mail.yahoo.com> Received: from [61.9.73.249] by web12801.mail.yahoo.com via HTTP; Mon, 29 Jul 2002 02:23:41 PDT Date: Mon, 29 Jul 2002 02:23:41 -0700 (PDT) From: amor san juan Subject: Hint geometry optimization To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello all; This had been a problem to me many months. Hope somebody patient enough to point out what molecular package can give cartesian coordinates for benzamidine as follows: ATOM1 C1 BEN 1 -1.853 14.311 16.658 ben C ATOM2 C2 BEN 1 -2.107 15.653 16.758 ben C ATOM3 H2 BEN 1 -2.573 16.191 15.916 ben H ATOM4 C3 BEN 1 -1.774 16.341 17.932 ben C ATOM5 H3 BEN 1 -1.983 17.421 18.014 ben H ATOM6 C4 BEN 1 -1.175 15.662 19.005 ben C ATOM7 H4 BEN 1 -0.914 16.201 19.931 ben H ATOM8 C5 BEN 1 -0.914 14.295 18.885 ben C ATOM9 H5 BEN 1 -0.441 13.744 19.715 ben H ATOM10 C6 BEN 1 -1.257 13.634 17.708 ben C ATOM11 H6 BEN 1 -1.051 12.555 17.611 ben H ATOM12 C7 BEN 1 -2.193 13.627 15.496 ben C ATOM13 N1 BEN 1 -2.797 14.235 14.491 ben N ATOM14 N2 BEN 1 -1.762 12.391 15.309 ben N ATOM15 H11 BEN 1 -3.039 13.707 13.640 ben H ATOM16 H12 BEN 1 -3.026 15.237 14.558 ben H ATOM17 H21 BEN 1 -1.287 11.890 16.073 ben H ATOM18 H22 BEN 1 -1.901 11.929 14.399 ben H I tried 2 different commercial molecular modeling package both have MM & semiempirical yet, I cant find result of conformation as above. Based from what I did these 2 commercial packages generated small cartesian coordinates. Would someone please show where is the problem.....advice some reading journals.....or even give any ideas. Sincerely, Amor __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Mon Jul 29 08:14:49 2002 Received: from web20207.mail.yahoo.com ([216.136.226.62]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6TCEnf25927 for ; Mon, 29 Jul 2002 08:14:49 -0400 Message-ID: <20020729121449.31164.qmail@web20207.mail.yahoo.com> Received: from [130.83.244.130] by web20207.mail.yahoo.com via HTTP; Mon, 29 Jul 2002 05:14:49 PDT Date: Mon, 29 Jul 2002 05:14:49 -0700 (PDT) From: Hatice Can Subject: MD with SYBYL To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear All, I try to do MD simulation with Sybyl 6.8. The system which will be simulated consists of an organic compound placed inside the zeolite supercage. I want to get conformers of organic compound when it is located inside the supercage of zeolite. I built the supercage and then I put the organic compound inside supercage. When I tried to built that system, I put the two molecules into two different areas, such as m1 and m2.For example, the organic compound is in m1 area and zeolite supercage is in m2 area. I am not quite sure that if the md simulation consider the molecule in m1 area, can program take into account of the forces can affect from which zeolite supercage to compound in area m1. If you would like to sent to me any advice or suggestions, I will be glad. Thank you in advance, Kind regards, Hatice __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Tue Jul 30 01:04:59 2002 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6U54xf22472 for ; Tue, 30 Jul 2002 01:04:59 -0400 Received: from [128.97.147.202] (ch-02.psnet.ucla.edu [128.97.147.202]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id g6U54PY11332; Mon, 29 Jul 2002 22:04:25 -0700 (PDT) Mime-Version: 1.0 Message-Id: Date: Mon, 29 Jul 2002 22:04:04 -0700 To: HOPOS-L@listserv.nd.edu From: Eric Scerri Subject: Philosophy of Chemistry Meeting in D.C. Content-Type: multipart/alternative; boundary="============_-1184117033==_ma============" --============_-1184117033==_ma============ Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: quoted-printable International Society for the Philosophy of Chemistry (ISPC) Georgetown University, Washington, DC. August 5 - 8, 2002 Plenary Sessions (Room 103 Healy Hall ) "Philosophy of Chemistry: From Infancy Towards Maturity,"J. Schummer, Univ. of Karlsruhe, Germany "Chemistry and the Structural Pattern of Explanation," R. Harr=E9, Georgetown University "The Issue of Reduction," J, van Brakel, K. U., Leuven, Belgium. "Mechanisms vs. Pathways in Biochemistry," L. Darden, Univ. of Maryland "Philosophical Confusion in Chemical Education Research," E. Scerri, UCLA "National Science Foundation Programs Related to Philosophy of Chemistry," A. Ellis, B Seely, NSF "Science and Art: Two Ways of Seeing," B. Berrie, National Gallery of Art, (West Bldg. Lecture Hall, NGA) Concurrent Sessions (103,104,105 Healy Hall) Philosophical Problems in Chemical Explanation "The Physicists, the Chemists and the Pragmatics of Explanation," R. =46. Hendry, The U. of Durham, UK "Natural Kinds, Explanation, and Essentialism in Chemistry," R. Vihalemm, The U. of Tartu, Estonia "A Sketch of Macroscopic Ontology," P. Needham, The U. of Stockholm, Sweden. "Sums or Products? Objects or States?" G. K. Vemulapalli, The Univ. of Arizona, AZ. "Can 'Things' Be Made Up of 'Features' or 'Properties'?" J. Earley, Georgetown Univ. Chemical Explanation Exemplified "Semi-empirical Models of Protein Folding: Construction and Evaluation in Theory Construction," J. Ramsey, Smith College "Chirality and Handedness: the Ruch 'Shoe-Potato' Dichotomy in Right-Left Classifications," R. B, King, Univ. of Ga. "Electronegativity and Base Strength," H. Raubenheimer, G. Heydenrych, Stellenbosch University, South Africa "Explanation in Organic Chemistry," W. Goodwin, Univiversity of California, Berkeley "Explaining Instrumental Techniques of Analytical Chemistry," D. Rothbart, George Mason University Representation, Visualization and Chemical Explanation "Beyond the Dimensionality of Visualization in Chemistry," A. Burewicz, N. Miranowicz, A. Mickiewicz U., Poland. "Molecular Aesthetics: From the Empirical to the Constitutive," T. Spector, The University of San Francisco "Writing As Thinking," J. Kovac, The University of Tennessee "A Mathematical Proposal for Linking the Natural Sciences," J. Chandler, Krasnow Institute, George Mason Univ. "Paradoxes of Measurement," P. Heelan, Georgetown University History and Chemical Explanation "Philosophy of Science and History3 of Science," F. M. Akeroyd, Bradford College, UK." "Richard Rufus' Theory of Mixture," M. Weisberg, Stanford University, CA. "Mendeleev's Discovery of the Periodic Law: the Origin and the Reception," M. Kaji, Tokyo Inst. of Technology, "Changing Identities and Shifting Domains: Development of NMR Spectroscopy 1956-1969", J. Roberts, VPI&SU. Chemical Explanation and Ultimate Concerns "Chemical Explanations, Metaphysical Realism and Tacit Knowledge," W. Brandt, Univ. of Wisc., Milwaukee. "Mind, Fitness, and Ambiguity: Chemical Emergences," R. Khuri, Falls Church, VA. "Chemical Explanations in Science and Spirituality," K. Hojo, Chiba, Japan. "Creation as a Principle in Chemistry," H. Vancik, The University of Zagreb, Croatia. " 'Complexification' and Self-Organization in a Process Philosophy of Union," J. Salmon, Loyola College. An Ethical Issue for Contemporary Chemistry," E. Klingsberg, Washington, DC Explanation and Chemical Physics "Physical Explanation of the Periodic Table," V. Ostrovsky, The University of St. Petersburg, Russia "Modal Domains and Quantal Protectorates," G. Farre, Georgetown University "Is the First Law Harmful?" G. Job, T. Lankau, The University of Hamburg, Germany "A Qualitative Account of the Chemical Bond in Terms of the Laws of Physics," S. Vollmer, H. Kincaid, U. Ala, Birmingham. "Is Chemistry a Gauge Theory?" J. Mattingly, Georgetown University Schedule at http://www.georgetown.edu/earleyj/ISPC.html Contact: Earleyj@ georgetown. -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri@chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.kluweronline.com/issn/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html --============_-1184117033==_ma============ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Philosophy of Chemistry Meeting in D.C.
International Society for the Philosophy of Chemistry (ISPC)
Georgetown University, Washington, DC.            August 5 - 8, 2002 
Plenary Sessions (Room 103 Healy Hall )
"Philosophy of Chemistry: From Infancy Towards Maturity,"J. Schummer, Univ. of Karlsruhe, Germany
"Chemistry and the Structural Pattern of Explanation," R. Harr=E9, Georgetown University
"The Issue of Reduction," J, van Brakel, K. U., Leuven, Belgium.
"Mechanisms vs. Pathways in Biochemistry," L. Darden, Univ. of Maryland
"Philosophical Confusion in Chemical Education Research," E. Scerri, UCLA
"National Science Foundation Programs Related to Philosophy of Chemistry," A. Ellis,  B Seely, NSF
"Science and Art: Two Ways of Seeing," B. Berrie, National Gallery of Art, (West Bldg. Lecture Hall, NGA)

Concurrent Sessions (103,104,105 Healy Hall)
Philosophical Problems in Chemical Explanation
"The Physicists, the Chemists and the Pragmatics of Explanation," R. F. Hendry, The U. of Durham, UK
"Natural Kinds, Explanation, and Essentialism in Chemistry," R. Vihalemm, The U. of Tartu, Estonia
"A Sketch of Macroscopic Ontology," P. Needham, The U. of Stockholm, Sweden.
"Sums or Products? Objects or States?" G. K. Vemulapalli, The Univ. of Arizona, AZ.
"Can 'Things' Be Made Up of 'Features' or 'Properties'?" J. Earley, Georgetown Univ.

 Chemical Explanation Exemplified
"Semi-empirical Models of Protein Folding: Construction and Evaluation in Theory Construction," J. Ramsey, Smith College
"Chirality and Handedness: the Ruch 'Shoe-Potato' Dichotomy in  Right-Left Classifications," R. B, King, Univ. of Ga.
"Electronegativity and Base Strength," H. Raubenheimer, G. Heydenrych, Stellenbosch University, South Africa
"Explanation in Organic Chemistry," W. Goodwin, Univiversity of California, Berkeley
"Explaining Instrumental Techniques of Analytical Chemistry," D. Rothbart, George Mason University

Representation, Visualization and Chemical Explanation
"Beyond the Dimensionality of Visualization in Chemistry," A. Burewicz, N. Miranowicz, A. Mickiewicz U., Poland.
"Molecular Aesthetics: From the Empirical to the Constitutive," T. Spector, The University of San =46rancisco
"Writing As Thinking," J. Kovac, The University of Tennessee
"A Mathematical Proposal for Linking the Natural Sciences," J. Chandler, Krasnow Institute, George Mason Univ.
"Paradoxes of Measurement," P. Heelan, Georgetown University

History and Chemical Explanation
"Philosophy of Science and History3 of Science,"  F. M. Akeroyd, Bradford College, UK."
"Richard Rufus' Theory of Mixture," M. Weisberg, Stanford University, CA.
"Mendeleev's Discovery of the Periodic Law: the Origin and the Reception," M. Kaji, Tokyo Inst. of  Technology,
"Changing Identities and Shifting Domains: Development of NMR Spectroscopy 1956-1969", J. Roberts, VPI&SU.

Chemical Explanation and Ultimate Concerns 
"Chemical Explanations, Metaphysical Realism and Tacit Knowledge," W. Brandt, Univ. of Wisc., Milwaukee.
"Mind, Fitness, and Ambiguity: Chemical Emergences,"  R. Khuri, Falls Church, VA.
"Chemical Explanations in Science and Spirituality,"  K. Hojo, Chiba, Japan.
"Creation as a Principle in Chemistry," H. Vancik, The University of Zagreb, Croatia.
" 'Complexification' and Self-Organization in a Process  Philosophy of Union,"  J. Salmon, Loyola College.
An Ethical Issue for Contemporary Chemistry," E. Klingsberg, Washington, DC

Explanation and Chemical Physics
"Physical Explanation of the Periodic Table," V. Ostrovsky, The University of St. Petersburg, Russia
"Modal Domains and Quantal Protectorates,"  G.  Farre, Georgetown University
"Is the First Law Harmful?" G. Job, T. Lankau, The University of Hamburg, Germany
"A Qualitative Account of the Chemical Bond in Terms of the Laws of Physics,"  S. Vollmer, H. Kincaid, U. Ala, Birmingham.
"Is Chemistry a Gauge Theory?" J. Mattingly, Georgetown University

Schedule at http://www.georgetown.edu/earleyj/ISPC.html   Contact: Earleyj@ georgetown.
--


Dr. Eric Scerri ,
UCLA,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Los Angeles,  CA 90095-1569
USA

E-mail :   scerri@chem.ucla.edu
tel:  310 206 7443
fax:  310 206 2061
Web Page:    http://www.chem.ucla.edu/dept/Faculty/scerri/index.html

Editor  of  Foundations of Chemistry
http://www.kluweronline.com/issn/1386-4238

Also see International Society for the Philosophy of Chemistry
http://www.georgetown.edu/earleyj/ISPC.html
--============_-1184117033==_ma============-- From chemistry-request@server.ccl.net Tue Jul 30 08:35:15 2002 Received: from web12803.mail.yahoo.com ([216.136.174.38]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6UCZFf30680 for ; Tue, 30 Jul 2002 08:35:15 -0400 Message-ID: <20020730123514.58748.qmail@web12803.mail.yahoo.com> Received: from [61.9.73.249] by web12803.mail.yahoo.com via HTTP; Tue, 30 Jul 2002 05:35:14 PDT Date: Tue, 30 Jul 2002 05:35:14 -0700 (PDT) From: amor san juan Subject: grid maps in autodock To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi all; If grid maps are specific only for ligand types then, does ligand charge dictates the presence of grid map values? Will this imply that relative positive charge ligand favors successful docking in AutoDock. Thanks for the enlightenment. Amor __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Mon Jul 29 13:09:50 2002 Received: from so.sd.lionbioscience.com ([209.68.255.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6TH9nf01187 for ; Mon, 29 Jul 2002 13:09:49 -0400 Received: from tempest.sd.lionbioscience.com (tempest.sd.lionbioscience.com [10.8.0.8]) by so.sd.lionbioscience.com (8.11.3/8.11.3) with ESMTP id g6TH9Dg18193 for ; Mon, 29 Jul 2002 10:09:19 -0700 (PDT) Received: by tempest.sd.lionbioscience.com with Internet Mail Service (5.5.2653.19) id ; Mon, 29 Jul 2002 10:09:03 -0700 Message-ID: From: Matthew Lee To: "'chemistry@ccl.net'" Subject: solution to empty affinity maps by autodock's autogrid Date: Mon, 29 Jul 2002 10:09:00 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C23722.A2102CE0" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C23722.A2102CE0 Content-Type: text/plain; charset="iso-8859-1" I have found the solution to my problem with Autodock 3.0's autogrid3. As reported earlier, autogrid3 was creating grid map files with all zero's (or whatever "constant" was defined to in the GPF file). Again, with one ligand, everything works fine, but in another ligand that happened to be much more flexible, I was having autogrid3 problems. The extra flexibility was unrelated to the problem. The problem lies in the "gridcenter" line of the GPF file. I used (as recommended by the manual) mkgpf3 to create the GPF file, but this mkgpf3 script defines the center of the grid based on the ligand's coordinates, not based on the protein's (the manual does not say it's doing this). Perhaps this is a feature in some instances?!?! In my problem case, the center of mass of the protein was about 60 Angstroms away from that of the ligand. Thus, wsing the GPF file created by mkgpf3 caused autogrid3 to produce useless affinity map files, presumably, because the protein was completely outside of the grid. Naturally, the affinities to every point in the grid would have been zero (or whatever you defined constant to be) if the protein is nowhere to be found in the grid. The most frustrating part of this was that there were no warning or error messages. In fact, the final message reported "autogrid3: Successful Completion." But of course, using these atom affinity maps leads to unsuccessful docking with autodock3. The solution is to edit the GPF file created by mkgpf3, using "gridcenter auto" instead of "gridcenter x.xx y.yy z.zz". The auto option, as documented, uses the macromolecule's center of mass as the grid center. --Matt Lee ******************************************************************* Matthew Randolph Lee, Ph.D. Computational Scientist phone: (858)410-6534 Lion Bioscience Inc. fax: (858)410-6665 9880 Campus Point Drive e-mail: matthew.lee@lionbioscience.com San Diego, CA 92121 ******************************************************************* ------_=_NextPart_001_01C23722.A2102CE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable solution to empty affinity maps by autodock's autogrid

        I have = found the solution to my problem with Autodock 3.0's autogrid3.  = As reported earlier, autogrid3 was creating grid map files with all = zero's (or whatever "constant" was defined to in the GPF = file).

        Again, = with one ligand, everything works fine, but in another ligand that = happened to be much more flexible, I was having autogrid3 = problems.  The extra flexibility was unrelated to the = problem.

        The = problem lies in the "gridcenter" line of the GPF file.  = I used (as recommended by the manual) mkgpf3 to create the GPF file, = but this mkgpf3 script defines the center of the grid based on the = ligand's coordinates, not based on the protein's (the manual does not = say it's doing this).  Perhaps this is a feature in some = instances?!?! 

        In my = problem case, the center of mass of the protein was about 60 Angstroms = away from that of the ligand.  Thus, wsing the GPF file created by = mkgpf3 caused autogrid3 to produce useless affinity map files, = presumably, because the protein was completely outside of the = grid.  Naturally, the affinities to every point in the grid would = have been zero (or whatever you defined constant to be) if the protein = is nowhere to be found in the grid.  The most frustrating part of = this was that there were no warning or error messages.  In fact, = the final message reported "autogrid3: Successful = Completion."  But of course, using these atom affinity maps = leads to unsuccessful docking with autodock3.

        The = solution is to edit the GPF file created by mkgpf3, using = "gridcenter auto" instead of "gridcenter x.xx y.yy = z.zz".  The auto option, as documented, uses the = macromolecule's center of mass as the grid center.

--Matt Lee

***************************************************************= ****
Matthew Randolph Lee, Ph.D.

Computational Scientist =         phone:  = (858)410-6534
Lion Bioscience Inc.    =         fax:    = (858)410-6665
9880 Campus Point Drive =       e-mail:  = matthew.lee@lionbioscience.com
San Diego, CA  92121
***************************************************************= ****

------_=_NextPart_001_01C23722.A2102CE0-- From chemistry-request@server.ccl.net Tue Jul 30 06:13:38 2002 Received: from delta.cti.unav.es ([159.237.12.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6UADbf28513 for ; Tue, 30 Jul 2002 06:13:38 -0400 Received: from alumni.unav.es ([159.237.72.47]) by delta.cti.unav.es (8.11.4/8.11.4) with ESMTP id g6UADZf30295 for ; Tue, 30 Jul 2002 12:13:35 +0200 Sender: jj@delta.cti.unav.es Message-ID: <3D467467.6C469021@alumni.unav.es> Date: Tue, 30 Jul 2002 13:11:35 +0200 From: Jose Javier Cuadrado X-Mailer: Mozilla 4.79 [en] (X11; U; IRIX64 6.5 IP30) X-Accept-Language: es, en, it, fr-FR MIME-Version: 1.0 To: CCL Subject: Secondary amines Content-Type: multipart/mixed; boundary="------------13A1D2B1FAB8AD6B1A5A2245" This is a multi-part message in MIME format. --------------13A1D2B1FAB8AD6B1A5A2245 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi to all I am working with a molecule that contains a secondary amine group. Its sustituents are: +a benzyl group +a phenyl ring I would like to know if that NH is a possible hydrogen bond acceptor. I have not found two much information. Could anybody tell me any reference about that class of secondary amines and their role as hydrogen bond acceptors? Thanks in advance --------------13A1D2B1FAB8AD6B1A5A2245 Content-Type: text/x-vcard; charset=us-ascii; name="jcuasan.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Jose Javier Cuadrado Content-Disposition: attachment; filename="jcuasan.vcf" begin:vcard n:Cuadrado Sanchez;Jose Javier x-mozilla-html:FALSE url:http://www.unav.es/organica/jj/ org:Universidad de Navarra;Dpto. Qca. Organica y Farmaceutica adr:;;C/Irunlarrea 1;Pamplona ;;31080;Espanna version:2.1 email;internet:jcuasan@alumni.unav.es x-mozilla-cpt:;26944 fn:Jose Javier Cuadrado Sanchez end:vcard --------------13A1D2B1FAB8AD6B1A5A2245-- From chemistry-request@server.ccl.net Tue Jul 30 12:16:12 2002 Received: from mail.chem.tamu.edu ([165.91.176.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6UGGCf03238 for ; Tue, 30 Jul 2002 12:16:12 -0400 Received: from [165.91.177.32] (account yubofan HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.5.2) with ESMTP id 1799487 for CHEMISTRY@ccl.net; Tue, 30 Jul 2002 11:16:30 -0500 Sender: yubo@ccl.net Message-ID: <3D46BC6A.385B8C7A@mail.chem.tamu.edu> Date: Tue, 30 Jul 2002 11:18:50 -0500 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Fixing bondlength doesn't work Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id g6UGGCf03239 Hi, everyone, I met a problem in recent days. I tried to use OPT=ModRedun option in G98 to fix a bondlength in my research system but it doesn't work for some of my cases. The related output is listed below: The following ModRedundant input section has been read: B 15 16 F 1.9000 Leave Link 101 at Tue Jul 30 15:58:11 2002, MaxMem= 67108864 cpu: 0.1 ---------------------------- ! Initial Parameters ! ! (Angstroms and Degrees) ! ------------------------ ------------------------- ! Name Definition Value Derivative Info. ! ----------------------------------------------------------------------------- ! R22 R(13,14) 1.0809 estimate D2E/DX2 ! ! R23 R(15,16) 1.9 estimate D2E/DX2 ! ! R24 R(15,36) 1.0453 estimate D2E/DX2 ! Is there any way to solve this problem? I tried cartesian and internal coordination input but both of them failed. Thanks in advance. Yubo -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ From chemistry-request@server.ccl.net Tue Jul 30 12:28:23 2002 Received: from mail.chem.tamu.edu ([165.91.176.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6UGSNf03603 for ; Tue, 30 Jul 2002 12:28:23 -0400 Received: from [165.91.177.32] (account yubofan HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.5.2) with ESMTP id 1799548 for CHEMISTRY@ccl.net; Tue, 30 Jul 2002 11:28:42 -0500 Sender: yubo@ccl.net Message-ID: <3D46BF43.859D1EFF@mail.chem.tamu.edu> Date: Tue, 30 Jul 2002 11:31:00 -0500 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: share memory problem for G98 on Linux Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id g6UGSNf03604 Hi, everyone, A share memory problem has always been bothering me for a long time since I ran G98 jobs on Linux boxes. Often, I have to kill running jobs manually to stop optimizations to wrong geometries. I just use "kill -9 'IDs of G98 job'". But, if I killed many times, I couldn't run parallel jobs any more. Share memory cannot be available at all. I have to restart the system to clean memory. Any advice. Thanks in advance Yubo -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ From chemistry-request@server.ccl.net Tue Jul 30 13:58:16 2002 Received: from mxout2.cac.washington.edu ([140.142.33.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6UHwGf05342 for ; Tue, 30 Jul 2002 13:58:16 -0400 Received: from mailscan-out2.cac.washington.edu (mailscan-out2.cac.washington.edu [140.142.33.17]) by mxout2.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.06) with SMTP id g6UHwBej009158 for ; Tue, 30 Jul 2002 10:58:11 -0700 Received: FROM dante17.u.washington.edu BY mailscan-out2.cac.washington.edu ; Tue Jul 30 10:58:11 2002 -0700 Received: from localhost (jzheng73@localhost) by dante17.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with ESMTP id g6UHwAK9080334 for ; Tue, 30 Jul 2002 10:58:11 -0700 Date: Tue, 30 Jul 2002 10:58:10 -0700 (PDT) From: "J. Zheng" cc: CHEMISTRY@ccl.net Subject: help, insert surface to Charmm In-Reply-To: <3D46BF43.859D1EFF@mail.chem.tamu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, CCLers: My research project is related to protein adsorption on the surfaces. In order to successfully finish this project, I write a FORTRAN code to deal with this system which includes protein, explicit waters, counter ions and surface by using CHARMM force field. Meanwhile, I try to use CHARMM to handle the same system. Now, my program is almost ready for the charged surface. In order to test the my program, I compared the my results with CHARMM's results for a protein and water system. Results are very close. but, my program is 30 times slower than CHARMM!! I use neighbour list to calculate nonbond interactions, while CHARMM uses cell list to do it. So, my qustions are 1) Except difference of neighbour list and cell list (I will change to cell list soon), is there anything I need to pay attention to avoid expensive calculations when I code program? any trick on the code? 2) Does anybody know how to add a surface to CHARMM? The surface coule be as simple as charged balls, or as complex as self-assembling monolayers. I can not find any tutorial or example to show how to do that from internet. Thank for taking your time and energy to read my questions. I will appreciate for your help. Jie ----------------------------------------------- | JIE ZHENG | | Department of Chemical Engineering | | University of Washington | | Seattle, WA 98105, USA | ----------------------------------------------- | Tel: (206) 616-6510 (o) | | Email: jzheng73@u.washington.edu | | Webpg: students.washington.edu/jzheng73 | ----------------------------------------------- From chemistry-request@server.ccl.net Tue Jul 30 12:46:22 2002 Received: from web20210.mail.yahoo.com ([216.136.226.65]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6UGkMf04014 for ; Tue, 30 Jul 2002 12:46:22 -0400 Message-ID: <20020730164621.3862.qmail@web20210.mail.yahoo.com> Received: from [130.83.244.130] by web20210.mail.yahoo.com via HTTP; Tue, 30 Jul 2002 09:46:21 PDT Date: Tue, 30 Jul 2002 09:46:21 -0700 (PDT) From: Hatice Can Subject: VERY LARGE Checkpoint file To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear All, I am using Gaussian98 for CASSCF calculations. I have a problem with reusing the checkpoint file.The size of checkpoint file is over 6MB. When I want to call it for using the geometry of molecule in another calculation, the file can not be opened. I will be glad for all the suggestions or advices. Thank you and best regards, Hatice __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Tue Jul 30 10:53:03 2002 Received: from md.huji.ac.il ([132.64.169.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6UEr3f01981 for ; Tue, 30 Jul 2002 10:53:03 -0400 Received: from md.huji.ac.il (localhost [127.0.0.1]) by md.huji.ac.il (8.12.2/8.12.2) with ESMTP id g6UEr5DF925212; Tue, 30 Jul 2002 17:53:05 +0300 (IDT) Received: from localhost (anvarr@localhost) by md.huji.ac.il (8.12.2/8.12.2/Submit) with ESMTP id g6UEr5s5923515; Tue, 30 Jul 2002 14:53:05 GMT Date: Tue, 30 Jul 2002 17:53:05 +0300 From: Anwar Rayan To: cc: Subject: free software which could assign atom types Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I have a molecule in two dimensions (connections between atoms) and another one in three dimensions (PDB format). Is there any free software which could assign atom types (hybridization state)? Lot of thanks in advance Anwar ------------------------------------- Dr. Anwar Rayan Department of Medicinal Chemistry School of Pharmacy The Hebrew University of Jerusalem P.O.B. 12065 Jerusalem 91120 Israel Tel: +972-2-6757540 Mobile: +972-55-848-338 Fax: +972-2-6757-076 Email: anvarr@md.huji.ac.il ------------------------------------- From chemistry-request@server.ccl.net Tue Jul 30 10:42:11 2002 Received: from cefni.aber.ac.uk ([144.124.16.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6UEgAf01800 for ; Tue, 30 Jul 2002 10:42:10 -0400 Received: from margaux.dcs.aber.ac.uk ([193.60.10.14] helo=aber.ac.uk) by cefni.aber.ac.uk with esmtp (Exim 3.21 #1) id 17ZYBV-0002GK-00; Tue, 30 Jul 2002 15:41:13 +0100 Sender: dle@aber.ac.uk Message-ID: <3D46A56F.2D0AB198@aber.ac.uk> Date: Tue, 30 Jul 2002 15:40:47 +0100 From: David Enot X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Hatice Can CC: chemistry@ccl.net Subject: Re: CCL:MD with SYBYL References: <20020729121449.31164.qmail@web20207.mail.yahoo.com> Content-Type: multipart/alternative; boundary="------------80FD0282ACFE7ACC3B83593C" X-Originating-IP: 193.60.10.14 X-Sophos-Scanned: from dle@aber.ac.uk virus scanned OK X-Originating-IP: 193.60.10.14 --------------80FD0282ACFE7ACC3B83593C Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, If you want to carry a DM within Sybyl, you will need to merge the 2 molecular areas. Use the sybyl command line, e.g. : merge m2 m1. The result will be in m1 and carry out the simulatin with m1. If you don't have the same coordinate systems, place manually your organic compound within the cage, use the command FREEZE in the STATIC MODE before merging m1 and m2. You can check the final result in mol2 file (by definition, its dynamic.mol2). Finally, I'm sure that using Sybyl is a good idea to do such simulations (Force field and DM algorithm). I think that lot of CCL's will indicate you a better protocole..... Regards David Hatice Can wrote: > Dear All, > > I try to do MD simulation with Sybyl 6.8. > The system which will be simulated consists of an > organic compound placed > inside the zeolite supercage. I want to get conformers > of organic > compound when it is located inside the supercage of > zeolite. I built the > supercage and then I put the organic compound inside > supercage. When I > tried to built that system, I put the two molecules > into two different > areas, such as m1 and m2.For example, the organic > compound is in m1 area > and zeolite supercage is in m2 area. > I am not quite sure that if the md simulation > consider the molecule in m1 area, can program take > into account of the > forces can affect from which zeolite supercage to > compound in area m1. > > If you would like to sent to me any advice or > suggestions, I will be glad. > > Thank you in advance, > > Kind regards, > > Hatice > > __________________________________________________ > Do You Yahoo!? > Yahoo! Health - Feel better, live better > http://health.yahoo.com > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ********************* David P. Enot, Ph D. *********************** * Department of Computer Science Work : +44 1970 622357 * * Computational Biology Group Fax : +44 1970 628536 * * U.W.A. - Aberystwyth SY23 3DB, UK Mobile : +44 7779 030629 * ********************* Email : dle@aber.ac.uk ********************* --------------80FD0282ACFE7ACC3B83593C Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit  
    Hello,

    If you want to carry a DM within Sybyl, you will need to merge the 2 molecular areas. Use the sybyl command line,
        e.g. : merge m2 m1. The result will be in m1 and carry out the simulatin with m1.
    If you don't have the same coordinate systems, place manually your organic compound within the cage, use the command FREEZE in the STATIC MODE before merging m1 and m2.
    You can check the final result in mol2 file (by definition, its dynamic.mol2).
    Finally, I'm sure that using Sybyl is a good idea to do such simulations (Force field and DM algorithm). I think that lot of CCL's will indicate you a better protocole.....

        Regards

           David

Hatice Can wrote:

Dear All,

I try to do MD simulation with Sybyl 6.8.
The system which will be simulated consists of an
organic compound placed
inside the zeolite supercage. I want to get conformers
of organic
compound when it is located inside the supercage of
zeolite. I built the
supercage and then I put the organic compound inside
supercage. When I
tried to built that system, I put the two molecules
into two different
areas, such as m1 and m2.For example, the organic
compound is in m1 area
and zeolite supercage is in m2 area.
 I am not quite sure that if the md simulation
consider the molecule in m1 area, can program take
into account of the
forces can affect from which zeolite supercage to
compound in area m1.

If you would like to sent to me any advice or
suggestions, I will be glad.

Thank you in advance,

Kind regards,

Hatice

__________________________________________________
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http://health.yahoo.com

-= This is automatically added to each message by mailing script =-
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-- 
 *********************  David P. Enot, Ph D.  ***********************
 *  Department of Computer Science        Work   : +44 1970 622357  *
 *  Computational Biology Group           Fax    : +44 1970 628536  *
 *  U.W.A. - Aberystwyth SY23 3DB, UK     Mobile : +44 7779 030629  *
 *********************  Email : dle@aber.ac.uk  *********************
  --------------80FD0282ACFE7ACC3B83593C-- From chemistry-request@server.ccl.net Tue Jul 30 14:12:06 2002 Received: from web12108.mail.yahoo.com ([216.136.172.28]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6UIC6f05721 for ; Tue, 30 Jul 2002 14:12:06 -0400 Message-ID: <20020730181206.84091.qmail@web12108.mail.yahoo.com> Received: from [200.31.15.122] by web12108.mail.yahoo.com via HTTP; Tue, 30 Jul 2002 11:12:06 PDT Date: Tue, 30 Jul 2002 11:12:06 -0700 (PDT) From: Paula Andrea Jaramillo Subject: dock in windows To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii can you help me with information about software dock 4.0 windows.i need some references about this program thank u . __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Tue Jul 30 19:53:55 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6UNrsf17932 for ; Tue, 30 Jul 2002 19:53:54 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id TAA27628; Tue, 30 Jul 2002 19:55:55 -0400 (EDT) Date: Tue, 30 Jul 2002 19:55:55 -0400 From: Rick Venable To: "J. Zheng" cc: CHEMISTRY@ccl.net Subject: Re: CCL:help, insert surface to Charmm In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 30 Jul 2002, J. Zheng wrote: > My research project is related to protein adsorption on the surfaces. > In order to successfully finish this project, I write a FORTRAN code to > deal with this system which includes protein, explicit waters, counter > ions and surface by using CHARMM force field. Meanwhile, I try to use > CHARMM to handle the same system. > > Now, my program is almost ready for the charged surface. In order to > test the my program, I compared the my results with CHARMM's results for a > protein and water system. Results are very close. but, my program is 30 > times slower than CHARMM!! I use neighbour list to calculate nonbond > interactions, while CHARMM uses cell list to do it. So, my qustions > are Actually, CHARMM uses a stored neighbor list, which gets updated frequently (e.g. every 10 or 20 integration steps). The frequency depends on the difference between CUTNB (list cutoff) and CTOFNB (potential forced to zero). There is a savings from not determining the non-bond list on every integration step. I've been using and writing code for CHARMM for over 15 years, and I'm not sure what you mean by a "cell list". CHARMM has a couple different methods for handling boundary conditions, one of which builds a second list of "image" atoms; these are periodic replicas of real atoms used for nonbond calculations with real atoms near the edge of the system. > 1) Except difference of neighbour list and cell list (I will change to > cell list soon), is there anything I need to pay attention to avoid > expensive calculations when I code program? any trick on the code? Avoid square roots, division, and trig fxns within inner loops. > 2) Does anybody know how to add a surface to CHARMM? The surface coule be > as simple as charged balls, or as complex as self-assembling > monolayers. I can not find any tutorial or example to show how to do > that from internet. It depends on what properties you want the surface to have. For simple elastic collisions, something like the MMFP module in CHARMM might work. For more sophisticated interactions with the surface, you might have to use a planar slab of fixed atoms of the appropriate types. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Tue Jul 30 15:58:24 2002 Received: from relay6.zonnet.nl ([62.58.50.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6UJwNf07018 for ; Tue, 30 Jul 2002 15:58:24 -0400 Received: from oac17.chem.vu.nl ([62.59.65.57]) by relay6.zonnet.nl (Netscape Messaging Server 4.15 ntr034 Mar 14 2002 21:29:48) with ESMTP id H02VH501.BD1; Tue, 30 Jul 2002 20:58:17 +0100 Date: Tue, 30 Jul 2002 21:57:50 +0200 Subject: Re: CCL:Hint geometry optimization Content-Type: multipart/alternative; boundary=Apple-Mail-2-359747108 Mime-Version: 1.0 (Apple Message framework v482) Cc: CHEMISTRY@ccl.net To: amor san juan From: Marcel Swart In-Reply-To: <20020729092341.90980.qmail@web12801.mail.yahoo.com> Message-Id: X-Mailer: Apple Mail (2.482) --Apple-Mail-2-359747108 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed This is straightforward.. The numbers you see on the lines are the Cartesian coordinates in=20 Angstroms !! I know cuz I tried to convert them into a C3D file (with my own=20 program), and succeeded: 18 title C 1 -1.853000 14.311000 16.658000 63 2 10 12 C 2 -2.107000 15.653000 16.758000 63 1 3 4 H 3 -2.573000 16.191000 15.916000 11 2 C 4 -1.774000 16.341000 17.932000 63 2 5 6 H 5 -1.983000 17.421000 18.014000 11 4 C 6 -1.175000 15.662000 19.005000 63 4 7 8 H 7 -0.914000 16.201000 19.931000 11 6 C 8 -0.914000 14.295000 18.885000 63 6 9 10 H 9 -0.441000 13.744000 19.715000 11 8 C 10 -1.257000 13.634000 17.708000 63 1 8 11 H 11 -1.051000 12.555000 17.611000 11 10 C 12 -2.193000 13.627000 15.496000 63 1 13 14 N 13 -2.797000 14.235000 14.491000 73 12 15 16 N 14 -1.762000 12.391000 15.309000 73 12 17 18 H 15 -3.039000 13.707000 13.640000 11 13 H 16 -3.026000 15.237000 14.558000 11 13 H 17 -1.287000 11.890000 16.073000 11 14 H 18 -1.901000 11.929000 14.399000 11 14 Any chemistry package can probably read the above coordinate set. If you want I can generate the coordinates also in another format. As for the hints on conversion of file formats, look for the Babel=20 program; links to it can be found in the CCL archives. On Monday, July 29, 2002, at 11:23 , amor san juan wrote: > Hello all; > > This had been a problem to me many months. Hope > somebody patient enough to point out what molecular > package can give cartesian coordinates for benzamidine > as follows: > > ATOM1 C1 BEN 1 -1.853 14.311 16.658 ben C > ATOM2 C2 BEN 1 -2.107 15.653 16.758 ben C > ATOM3 H2 BEN 1 -2.573 16.191 15.916 ben H > ATOM4 C3 BEN 1 -1.774 16.341 17.932 ben C > ATOM5 H3 BEN 1 -1.983 17.421 18.014 ben H > ATOM6 C4 BEN 1 -1.175 15.662 19.005 ben C > ATOM7 H4 BEN 1 -0.914 16.201 19.931 ben H > ATOM8 C5 BEN 1 -0.914 14.295 18.885 ben C > ATOM9 H5 BEN 1 -0.441 13.744 19.715 ben H > ATOM10 C6 BEN 1 -1.257 13.634 17.708 ben C > ATOM11 H6 BEN 1 -1.051 12.555 17.611 ben H > ATOM12 C7 BEN 1 -2.193 13.627 15.496 ben C > ATOM13 N1 BEN 1 -2.797 14.235 14.491 ben N > ATOM14 N2 BEN 1 -1.762 12.391 15.309 ben N > ATOM15 H11 BEN 1 -3.039 13.707 13.640 ben H > ATOM16 H12 BEN 1 -3.026 15.237 14.558 ben H > ATOM17 H21 BEN 1 -1.287 11.890 16.073 ben H > ATOM18 H22 BEN 1 -1.901 11.929 14.399 ben H > > I tried 2 different commercial molecular modeling > package both have MM & semiempirical yet, I cant find > result of conformation as above. Based from what I did > these 2 commercial packages generated small cartesian > coordinates. > > Would someone please show where is the > problem.....advice some reading journals.....or even > give any ideas. > > Sincerely, > Amor > > __________________________________________________ > Do You Yahoo!? > Yahoo! Health - Feel better, live better > http://health.yahoo.com > > > -=3D This is automatically added to each message by mailing script =3D- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To=20= > Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan:=20 > jkl@ccl.net > > > > > > > =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96 Marcel Swart Organische en Anorganische Chemie Faculteit der Exacte Wetenschappen Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands F +31-(0)20-4447488 E swart@chem.vu.nl W http://go.to/m.swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-2-359747108 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 This is straightforward.. The numbers you see on the lines are the Cartesian coordinates in Angstroms !! I know cuz I tried to convert them into a C3D file (with my own program), and succeeded: 18 title C 1 -1.853000 14.311000 16.658000 63 2 10 12 C 2 -2.107000 15.653000 16.758000 63 1 3 4 H 3 -2.573000 16.191000 15.916000 11 2 C 4 -1.774000 16.341000 17.932000 63 2 5 6 H 5 -1.983000 17.421000 18.014000 11 4 C 6 -1.175000 15.662000 19.005000 63 4 7 8 H 7 -0.914000 16.201000 19.931000 11 6 C 8 -0.914000 14.295000 18.885000 63 6 9 10 H 9 -0.441000 13.744000 19.715000 11 8 C 10 -1.257000 13.634000 17.708000 63 1 8 11 H 11 -1.051000 12.555000 17.611000 11 10 C 12 -2.193000 13.627000 15.496000 63 1 13 14 N 13 -2.797000 14.235000 14.491000 73 12 15 16 N 14 -1.762000 12.391000 15.309000 73 12 17 18 H 15 -3.039000 13.707000 13.640000 11 13 H 16 -3.026000 15.237000 14.558000 11 13 H 17 -1.287000 11.890000 16.073000 11 14 H 18 -1.901000 11.929000 14.399000 11 14 Any chemistry package can probably read the above coordinate set. If you want I can generate the coordinates also in another format. As for the hints on conversion of file formats, look for the Babel program; links to it can be found in the CCL archives. On Monday, July 29, 2002, at 11:23 , amor san juan wrote: Hello all; This had been a problem to me many months. Hope somebody patient enough to point out what molecular package can give cartesian coordinates for benzamidine as follows: ATOM1 C1 BEN 1 -1.853 14.311 16.658 ben C ATOM2 C2 BEN 1 -2.107 15.653 16.758 ben C ATOM3 H2 BEN 1 -2.573 16.191 15.916 ben H ATOM4 C3 BEN 1 -1.774 16.341 17.932 ben C ATOM5 H3 BEN 1 -1.983 17.421 18.014 ben H ATOM6 C4 BEN 1 -1.175 15.662 19.005 ben C ATOM7 H4 BEN 1 -0.914 16.201 19.931 ben H ATOM8 C5 BEN 1 -0.914 14.295 18.885 ben C ATOM9 H5 BEN 1 -0.441 13.744 19.715 ben H ATOM10 C6 BEN 1 -1.257 13.634 17.708 ben C ATOM11 H6 BEN 1 -1.051 12.555 17.611 ben H ATOM12 C7 BEN 1 -2.193 13.627 15.496 ben C ATOM13 N1 BEN 1 -2.797 14.235 14.491 ben N ATOM14 N2 BEN 1 -1.762 12.391 15.309 ben N ATOM15 H11 BEN 1 -3.039 13.707 13.640 ben H ATOM16 H12 BEN 1 -3.026 15.237 14.558 ben H ATOM17 H21 BEN 1 -1.287 11.890 16.073 ben H ATOM18 H22 BEN 1 -1.901 11.929 14.399 ben H=20 I tried 2 different commercial molecular modeling package both have MM & semiempirical yet, I cant find result of conformation as above. Based from what I did these 2 commercial packages generated small cartesian coordinates. Would someone please show where is the problem.....advice some reading journals.....or even give any ideas. Sincerely, Amor __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com -=3D This is automatically added to each message by mailing script =3D- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 Marcel Swart Organische en Anorganische Chemie Faculteit der Exacte Wetenschappen Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands F +31-(0)20-4447488 E swart@chem.vu.nl W http://go.to/m.swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96= --Apple-Mail-2-359747108--