From chemistry-request@server.ccl.net Mon Nov 20 12:29:32 2000 Received: from server.nybc.org (server.nybc.org [192.94.249.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA19026 for ; Mon, 20 Nov 2000 12:29:31 -0500 Received: from iris.nybc.org ([192.94.249.42]) by server.nybc.org (Netscape Mail Server v2.0) with ESMTP id AAA10151; Mon, 20 Nov 2000 12:28:27 -0400 Received: from nybc.org (localhost [127.0.0.1]) by iris.nybc.org (SGI-8.9.3/8.9.3) with ESMTP id MAA10557; Mon, 20 Nov 2000 12:29:26 -0500 (EST) Sender: debnath@iris.nybc.org Message-ID: <3A195F75.72008F6@nybc.org> Date: Mon, 20 Nov 2000 12:29:26 -0500 From: Asim Kumar Debnath Organization: New York Blood Center X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: "Shobe, Dave" CC: chemistry@ccl.net Subject: Re: CCL:intro to qspar References: <157A51F55AAAD3119CD70008C7B1629D6386C1@lvlxch01.unitedcatalysts.com> Content-Type: multipart/alternative; boundary="------------F6DACB37C5C76734E2DF5129" --------------F6DACB37C5C76734E2DF5129 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Dave: I think Corwin Hansch's book will be an excellent choice but for beginners I would strongly suggest another book Edited by Hansch, Sammes and Taylor, " Comprehensive Medicinal Chemistry - Vol 4 from Pergaman". This volume covers almost every aspect of fundamental QSAR principles including history and background. Each chapter also has a great compilation of references that will be very valuable for further reading. But this book is not cheap either. You might get from some libraries. Hope this helps. Asim Debnath "Shobe, Dave" wrote: > I would like to teach myself QSPAR (quantitative > structure/properties/activity relationships) and am looking for a "textbook" > appropriate for self-study. Does anyone have any recommendations? Two > possibilities I've found are: > > Molecular Descriptors in QSAR/QSPR including CD-ROM > Mati Karelson (John Wiley & Sons, Feb. 2000) $195.00 > > Exploring QSAR (2 volumes) > Corwin Hansch and Albert Leo (Am. Chem. Soc., March 1995) $163.00 > > If anyone has seen these and can review them regarding: > (1) suitability as an introduction to the subject > (2) usefulness as a reference later > (3) value--these seem pricey even for scientific textbooks > it would be appreciated. > > I am not employed in the pharmaceutical industry (nor am I planning to > unless things turn sour at my current job), but I would like to round out my > "chemoinformatics" knowledge, as my background includes computational > chemistry and information science. > > --David Shobe > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ======================================================================= *** *** **** Asim K. Debnath, Ph.D. **** Lindsley F. Kimball Research Institute **** *** The New York Blood Center **** **** 310 E 67 Th Street **** ** **** New York, NY 10021 **** **** **** Tel. (212) 570-3373 **** ** **** Fax. (212) 570-3299 **************** E-mail: adebnath@nybc.org ************** ======================================================================== --------------F6DACB37C5C76734E2DF5129 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Dave:
    I think Corwin Hansch's book will be an excellent choice but for beginners I would strongly suggest another book Edited by Hansch, Sammes and Taylor, " Comprehensive Medicinal Chemistry - Vol 4 from Pergaman". This volume covers almost every aspect of fundamental QSAR principles including history and background. Each chapter also has a great compilation of references that will be very valuable for further reading. But this book is not cheap either. You might get from some libraries.
    Hope this helps.

Asim Debnath

"Shobe, Dave" wrote:

I would like to teach myself QSPAR (quantitative
structure/properties/activity relationships) and am looking for a "textbook"
appropriate for self-study. Does anyone have any recommendations?  Two
possibilities I've found are:

Molecular Descriptors in QSAR/QSPR including CD-ROM
Mati Karelson (John Wiley & Sons, Feb. 2000) $195.00

Exploring QSAR (2 volumes)
Corwin Hansch and Albert Leo (Am. Chem. Soc., March 1995) $163.00

If anyone has seen these and can review them regarding:
(1) suitability as an introduction to the subject
(2) usefulness as a reference later
(3) value--these seem pricey even for scientific textbooks
it would be appreciated.

I am not employed in the pharmaceutical industry (nor am I planning to
unless things turn sour at my current job), but I would like to round out my
"chemoinformatics" knowledge, as my background includes computational
chemistry and information science.

--David Shobe

-= This is automatically added to each message by mailing script =-
CHEMISTRY@ccl.net -- To Everybody    |   CHEMISTRY-REQUEST@ccl.net -- To Admins
MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
CHEMISTRY-SEARCH@ccl.net -- archive search    |    Gopher: gopher.ccl.net 70
Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net

-- 



=======================================================================

             ***
             ***                
            ****                Asim K. Debnath, Ph.D.
           ****                 Lindsley F. Kimball Research Institute 
          ****  ***             The New York Blood Center
         ****    ****           310 E 67 Th Street
        ****  **  ****          New York, NY 10021
       ****  ****  ****         Tel. (212) 570-3373
      ****    **    ****        Fax. (212) 570-3299
       ****************         E-mail: adebnath@nybc.org
        **************                                  
                                        
========================================================================
  --------------F6DACB37C5C76734E2DF5129-- From chemistry-request@server.ccl.net Mon Nov 20 15:51:27 2000 Received: from web9205.mail.yahoo.com (web9205.mail.yahoo.com [216.136.129.38]) by server.ccl.net (8.8.7/8.8.7) with SMTP id PAA19921 for ; Mon, 20 Nov 2000 15:51:23 -0500 Message-ID: <20001120204918.71946.qmail@web9205.mail.yahoo.com> Received: from [141.161.229.35] by web9205.mail.yahoo.com; Mon, 20 Nov 2000 12:49:18 PST Date: Mon, 20 Nov 2000 12:49:18 -0800 (PST) From: Jiansuo Wang Subject: DOCK program on Linux? To: chemistry@ccl.net Cc: jiansuowang@yahoo.com MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear cclers, DOCK, developed by Professor Kuntz's group, uses database and docking procedure to suggest moleclues targeted at a given receptor. Does anyone successfully compile the DOCK program on Linux? Any comments or suggestion are appreciated. Thanks. Sincerely yours Jiansuo Wang ------------------------------------ Dr. Jiansuo Wang Georgetown University Medical Center Washington DC, 20007 ------------------------------------ __________________________________________________ Do You Yahoo!? Yahoo! Calendar - Get organized for the holidays! http://calendar.yahoo.com/ From chemistry-request@server.ccl.net Tue Nov 21 01:59:19 2000 Received: from dns2.seanet.com (dns2.seanet.com [199.181.164.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA22044 for ; Tue, 21 Nov 2000 01:59:19 -0500 Received: from biggeek (ip-64-38-140-3.dialup.seanet.com [64.38.140.3]) by dns2.seanet.com (8.9.3/8.9.0) with SMTP id WAA29510; Mon, 20 Nov 2000 22:58:28 -0800 (PST) Message-ID: <003401c05388$54aaa0e0$01808080@biggeek> From: "Mark A. Thompson" To: "env chem" , "organic chem" , "nat prod" , "GAMESS" , "chem web" , "CCL" , "chem ed2" , "chem ed" Cc: Subject: New ArgusLab beta release #3 Date: Mon, 20 Nov 2000 22:57:28 -0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_002F_01C05345.41907950" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 This is a multi-part message in MIME format. ------=_NextPart_000_002F_01C05345.41907950 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 There is a new release of ArgusLab version 2, beta build 3 available at: http://www.seanet.com/~mthompson/ArgusLab This build includes a fix for the install program. The new install is a self-contained executable that contains the Microsoft Installer runtime. enjoy Mark Thompson ArgusLab is a molecular modeling program for Microsoft Windows operating = systems. Overview of 2.0 features: ----------------------------- 1. Interactive 3D Molecule Builder with: Interactive 3D manipulator Fragment Library Beautify Geometry Automatically Add/Hide/Delete Hydrogens Cut & Paste Supports Multiple-Level Undo/Redo. Multiple Rendering Styles for Atoms and Bonds Geometry Monitors 2. Calculation Types Single-Point Energies Optimize Geometries Electronic Excitation Spectra Self Consistent Reaction Field (SCRF) Solvent Model for = Electronic Spectra 3. Molecular Mechanics=20 Universal Force Field (UFF) for the entire periodic table 4. Quantum Mechanics Extended Huckel for entire periodic table MNDO, AM1, and PM3 semi-empirical Hamiltonians INDO1/s semi-empirical Hamiltonian Restricted and Unrestricted Hartree-Fock SCF 5. File Types: supports XYZ, PDB, and ArgusLab XML file formats. 6. HTML Help 7. No size limitations for molecules or calculations other than = available system resources 8. Multi-threaded architecture allows multiple molecules opened = simultaneously and running calculations 9. Runs on Windows 95/98, Windows NT 4.0, Windows 2000 ------=_NextPart_000_002F_01C05345.41907950 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 
There is a new release of = ArgusLab=20 version 2, beta build 3
available at:
 
http://www.seanet.com/= ~mthompson/ArgusLab
 
 
This build includes a fix for = the install=20 program.  The new install
is a self-contained = executable that=20 contains the Microsoft
Installer = runtime.
 
enjoy
Mark Thompson
 
 
 
 
ArgusLab is a molecular = modeling program=20 for Microsoft Windows operating systems.
 
Overview of 2.0 = features:
-----------------------------
1. Interactive 3D Molecule = Builder=20 with:
        Interactive 3D=20 manipulator
        Fragment=20 Library
        Beautify=20 Geometry
        Automatically = Add/Hide/Delete=20 Hydrogens
        Cut &=20 Paste
        Supports Multiple-Level=20 Undo/Redo.
        Multiple Rendering = Styles=20 for Atoms and Bonds
        Geometry=20 Monitors

 
2. Calculation=20 Types
        Single-Point=20 Energies
        Optimize=20 Geometries
        Electronic = Excitation=20 Spectra
        Self Consistent = Reaction Field=20 (SCRF) Solvent Model for Electronic Spectra

 
3. Molecular=20 Mechanics 
        Universal Force = Field=20 (UFF) for the entire periodic table

 
4. Quantum=20 Mechanics
        Extended Huckel for = entire=20 periodic table
        MNDO, AM1, and = PM3=20 semi-empirical Hamiltonians
        = INDO1/s=20 semi-empirical Hamiltonian
        = Restricted=20 and Unrestricted Hartree-Fock SCF

 
5. File Types: supports XYZ, = PDB, and=20 ArgusLab XML file formats.
6. HTML Help
7. No size limitations for = molecules or=20 calculations other than available system resources
8. Multi-threaded = architecture allows=20 multiple molecules opened simultaneously and running=20 calculations
9. Runs on Windows 95/98, = Windows NT 4.0,=20 Windows 2000
------=_NextPart_000_002F_01C05345.41907950-- From chemistry-request@server.ccl.net Tue Nov 21 03:36:13 2000 Received: from ibms.ibms.sinica.edu.tw (ibms.ibms.sinica.edu.tw [140.109.40.101]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA22787 for ; Tue, 21 Nov 2000 03:36:12 -0500 From: syn@ibms.sinica.edu.tw Received: from ibms (ibms [140.109.40.101]) by ibms.ibms.sinica.edu.tw (8.9.3+Sun/8.9.3) with ESMTP id QAA03868 for ; Tue, 21 Nov 2000 16:30:02 +0800 (CST) Date: Tue, 21 Nov 2000 16:30:01 +0800 (CST) X-Sender: syn@ibms To: chemistry@ccl.net Subject: QM/MM in CHARMM In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I `ve try to use a QM/MM block of CHARMM programm but I had a problem. We use a CHARMM 27b1 version and I create the input file according to manual i.e. first block is generation of molecule ( for test case I use an ethane) second block is quantum command and chhosing of link atom, in my case it is one of the carbon: QUANTUM SELE BYNU 1:4 END GLNK SELE BYNU 8 END AM1 MINI SD NSTEP 1000 npr 10 ******* At this step I had a permanent fatal error: QATLAB is not defined, no EXPR group...Does it means that I need to use ADDL command or not? Can anybody help to fix this problem because previous version of CHARMM (CHARMM 24b2) had another syntax and have no GLNK facilities? Best regards, Sergey Sergey Noskov Institute of BioMedical Sciences Academia Sinica Taipei 11529,Taiwan R.O.C. tel:886-2-27899043 (work) 886-2-26510783 (home) fax:886-2-27887641 e-mail:syn@ibms.sinica.edu.tw From chemistry-request@server.ccl.net Tue Nov 21 08:45:33 2000 Received: from fbcb.unl.edu.ar (root@fbcb.unl.edu.ar [170.210.10.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA25036 for ; Tue, 21 Nov 2000 08:45:31 -0500 From: sgaray@fbcb.unl.edu.ar Received: from qorgbio1.unl.edu.ar (qorgbio1.unl.edu.ar [170.210.10.38]) by fbcb.unl.edu.ar (8.8.7/8.8.7) with SMTP id KAA00072 for ; Tue, 21 Nov 2000 10:58:47 -0300 Message-Id: <200011211358.KAA00072@fbcb.unl.edu.ar> To: chemistry@ccl.net Date: Tue, 21 Nov 2000 10:49:45 -0300 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Question X-Confirm-Reading-To: sgaray@fbcb.unl.edu.ar X-pmrqc: 1 Priority: urgent X-mailer: Pegasus Mail for Win32 (v3.01b) Hi to all. My name is Alberto Sergio Garay I will begin to work in a MD of Biomembranes at the Facultad de Bioquimica y Cs. Biologicas. Universidad Nacional del Litoral. Santa Fe. Argentina I will begin to work in a MD of Biomembranes and I need to parametrize a probe for EPR spectroscopy. May be someone parametrized some molecule like this: 1- myristoyl-2-[6-(4,4-dimethyloxazolidine-N-oxyl)myritoyl]-sn-glycero- 3-phosphocholine or may be could give some information about my problem. thank you to all. From chemistry-request@server.ccl.net Tue Nov 21 10:06:55 2000 Received: from bellatrix.pcl.ox.ac.uk (root@bellatrix.pcl.ox.ac.uk [163.1.35.134]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA25388 for ; Tue, 21 Nov 2000 10:06:52 -0500 Received: from localhost (ben@localhost) by bellatrix.pcl.ox.ac.uk (8.9.3/8.8.7) with ESMTP id PAA23244; Tue, 21 Nov 2000 15:06:26 GMT Date: Tue, 21 Nov 2000 15:06:26 +0000 (GMT) From: Ben Webb To: syn@ibms.sinica.edu.tw cc: chemistry@ccl.net Subject: Re: CCL:QM/MM in CHARMM In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 21 Nov 2000 syn@ibms.sinica.edu.tw wrote: > At this step I had a permanent fatal error: QATLAB is not defined, no > EXPR group...Does it means that I need to use ADDL command or not? Can > anybody help to fix this problem because previous version of CHARMM > (CHARMM 24b2) had another syntax and have no GLNK facilities? You don't say which platform you're running CHARMM on, so this makes it difficult to determine what your problem is. However, this "undefined QATLAB" problem occurs with CHARMM on GNU platforms (e.g. Linux) and has only been fixed as of c27b3/c28a3. The fix is relatively straightforward; add GNU to the ##IF statement immediately before "external QMMMDATA" in qmset.src, and recompile all of the files in the quantum directory with the "-finit-local-zero -fno-automatic" compiler flags (if this is not done the code fails to carry out an energy calculation). Hope this helps... Ben From chemistry-request@server.ccl.net Tue Nov 21 19:50:14 2000 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.8.7/8.8.7) with SMTP id TAA27842 for ; Tue, 21 Nov 2000 19:44:07 -0500 Received: from iris.sipp.ac.cn (202.127.25.133) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Wed, 22 Nov 2000 08:48:00 +0800 Sender: user@ccl.net Message-ID: <3A1B15EA.B1877F22@iris.sipp.ac.cn> Date: Wed, 22 Nov 2000 08:40:10 +0800 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: summary: adding hydrogen using charmm Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 7bit Hello, everyone: The day before yesterday, I post a problem about adding hydrogen to a pdb file using charmm. And in the past two days, I received many reply about my problem, and now I solve the problem. In fact, my problem is not the problem of adding hydrogen, but reading coordinate. I put a segid name of 'prot' in the last column of pdb file, and the problem was solved. Here I put all the reply in this email, and thank all of you who reply me. ------------------------------------------------------------------------------------- From: ablondel@pasteur.fr You have a problem reading the coordinate (no N,CA,C,O for amino acid 1...). There must be a name mismatch between psf and pdb. Change the pdb accordingly, if appropriate. It seems reasonable that you cannot build the Hs on a missing N. An advise "learn" to read the output of charmm carefully. The problem is most of the time signalled but it may be hundreds of lines before the crash. As a rule of thumb read every line of output and correct the input until you don't have any more warnings that may cause a problem. From: alex@outerbanks.umaryland.edu the charmm pdb reader is not great. one suggestion is to write the coordinates (write coor pdb unit xx) after doing the generation. all the coordinates will be 9999. but it will allow you to see the format that charmm is looking for. also, do ic fill ic para ic build before hbuild From: surjit@lctn.u-nancy.fr Charmm needs a pdb file that has a segname as the last column. So you need to modify the input pdb file a little for Charmm to appreciate that. For eg here is a line from a normal pdb file and the corresponding one that Charmm appreciates. Normal pdb ATOM 1 O1 BTN 1 0.311 -4.640 15.789 1.00 0.00 Charmm PDB ATOM 1 O1 BTN 1 0.311 -4.640 15.789 1.00 0.00 BTN The last column is the segname is call in the psf file. From: lozg@mail.rochester.edu It seems that your input file for charmm is ok, but the PDB file is not ok. Generally I will encounter this problem when I just download a structure from PDB and throw it to CHARMM. I don't know exactly what is going on, but it is quite possible that the format of the PDB is not acceptable by CHARMM. So, what I do is, write a Fortran program to change the downloaded PDB file to a card file, and serve the CHARMM with the card file. From: rvenable@gandalf.cber.nih.gov Actually, you seem to be having a problem with reading coords from the PDB file. Also, your IC commands aren't quite right (you don't want IC FILL), and should probably precede the HBUILD-- you *must* make sure all heavy atoms have coords before calling HBUILD. Here's the way I read in a PDB file for a peptide: open unit 3 read card name meltna.pdb read sequ pdb unit 3 rewind unit 3 gener a setup warn first glyp last ct2 ! SETUP UNIVERSAL COORD I/O FOR PDB; BETTER THAN read coor pdb read univ pdb w 61 6 end read coor univ unit 3 sele .not. type H* end close unit 3 ic param ! FILL IN MISSING VALUES FROM PARAM FILE ic purge ! CLEANUP IC TABLE ic build ! BUILD COORDS FROM IC ! FORCE REBUILD OF ALL H ATOM COORDS coor init sele type H* end hbuild sele type H* end From: syn@ibms.sinica.edu.tw> ! read in NMR coordinates OPEN READ UNIT 11 CARD NAME - /home/user/marios/rnase/crd/1rch_15.crd READ COOR CARD UNIT 11 FREE CLOSE UNIT 11 ! build missing coordinates IC FILL PRESERVE IC PARAMETERS IC BUILD ! place the hydrogens HBUILD It is better to use CHARMM use their own coordinate file. From: torsten.becker@iwr.uni-heidelberg.de your problem is not building the hydrogens, but reading the coordinates. Charmm does not read in the coordinates of your system: > ** WARNING ** For atom in coordinate file, could not find residue in > PSF, and is thus ignored: > > SEGID= RESID=1 RESNAME= GLU TYPE= N > *** LEVEL 1 WARNING *** BOMLEV IS 0 > charmm does read the coordinates from your pdb, but cannot find a corresponding atom in the system you did setup. Charmm identifies a system via a segment ID (segid). Since charmm stells you 'segid= ', i guess you forgot to specify the segid in your pdb file. You gave your first segment the name 'prot' . This name must be specified in your pdb file, when reading coordinates from it. I don't know the exact format now, but in each ATOM/HETATOM line after the B-factor entry you have to put prot. From: ed@bioorganic.ucsb.edu> Hello, you need to rewind unit 1 before you can read the coordinates. When you use the " read sequ pdb" command it reads to the end of the file. When the second command "read coor pdb" comes the file is still at the end so it finds no coordinates. The following should work ! Read sequence from the PDB coordinate file open unit 1 card read name 1pef.pdb read sequ pdb unit 1 ! now generate the PSF and also the IC table (SETU keyword) generate prot setu ! read in pdb coordinate file rewind unit 1 ! rewinding the coordinate file open unit 1 card read name 1pef.pdb read coor pdb unit 1 close unit 1 ------------------------------------------------------------------------ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Xiang Mao | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~