From chemistry-request@server.ccl.net Mon Sep 10 01:08:18 2001 Received: from exstudent9.city.unisa.edu.au ([130.220.84.78]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8A58HM16616 for ; Mon, 10 Sep 2001 01:08:18 -0400 Received: by exstudent9.city.unisa.edu.au with Internet Mail Service (5.5.2653.19) id ; Mon, 10 Sep 2001 14:38:15 +0930 Message-ID: From: "Sorich, Michael Joseph - SORMJ001" To: "'chemistry@ccl.net.'" Subject: SUMMARY: SOMFA and CSSR file format Date: Mon, 10 Sep 2001 14:38:09 +0930 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C139B6.95478D10" 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_01C139B6.95478D10 Content-Type: text/plain I wrote previously concerning a problem getting a 3D QSAR program SOMFA (freely available at http://bellatrix.pcl.ox.ac.uk/downloads/) to input .cssr files. Many thanks to Tamas Gunda and Hans Martin Senn for their generous help. 1) The problem lies with the .cssr definition used by the SOMFA program. It requires a group number to be present at the end of each Record 5 (one for each atom in the molecule). Most programs do not include this field when generating .cssr files. The SOMFA program does not use the group number in any way, so adding any integer at the the end of each Record 5 will allow the file to be used without error. I have written a short script which will add an integer in the correct position to a .cssr file (available upon request) 2) Descriptions of the .cssr file format can be found at: The Chem-X Reference Manual Index. Page down until you reach "CSSR file format" http://www-fbsc.ncifcrf.gov/compenv/app_soft/man/chemx/document/refindex.htm The Cerius2 manual http://ir.chem.cmu.edu/chem560/docs/msi/modenv/D_Files.html Michael Sorich PhD Student School of Pharmaceutical, Molecular and Biomedical Sciences University of South Australia email: sormj001@students.unisa.edu.au or mike_sorich@hotmail.com ------_=_NextPart_001_01C139B6.95478D10 Content-Type: text/html Content-Transfer-Encoding: quoted-printable SUMMARY: SOMFA and CSSR file format

I wrote previously concerning a problem getting a 3D = QSAR program
SOMFA (freely available at http://bellatrix.pcl.ox.ac.uk/downloads/)
to input .cssr files.

Many thanks to Tamas Gunda and Hans Martin Senn for = their generous
help.
    
1) The problem lies with the .cssr definition used = by the SOMFA
program. It requires a group number to be present at = the end of
each Record 5 (one for each atom in the molecule). = Most programs
do not include this field when generating .cssr = files. The SOMFA
program does not use the group number in any way, so = adding any
integer at the the end of each Record 5 will allow = the file to
be used without error. I have written a short script = which
will add an integer in the correct position to a = .cssr file
(available upon request)
 
2) Descriptions of the .cssr file format can be = found at:

The Chem-X Reference Manual Index. Page down until = you reach "CSSR file format"
http://www-fbsc.ncifcrf.gov/compenv/app_soft/man/chemx= /document/refindex.htm

The Cerius2 manual
http://ir.chem.cmu.edu/chem560/docs/msi/modenv/D_Files= .html



Michael Sorich

PhD Student
School of Pharmaceutical, Molecular and Biomedical = Sciences
University of South Australia
email: sormj001@students.unisa.edu.au
or mike_sorich@hotmail.com

------_=_NextPart_001_01C139B6.95478D10-- From chemistry-request@server.ccl.net Sun Sep 9 21:43:59 2001 Received: from hunny.INS.cwru.edu (root@[129.22.8.186]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8A1hwM12320 for ; Sun, 9 Sep 2001 21:43:58 -0400 Received: from gavin (chem51286.CHEM.CWRU.Edu [129.22.129.217]) by hunny.INS.cwru.edu with SMTP (8.11.6+cwru/CWRU-3.8) id f8A1hxD12594; Sun, 9 Sep 2001 21:43:59 -0400 (EDT) (from hxt10@po.cwru.edu for ) Message-ID: <001901c1399a$c392a900$d9811681@cwru.edu> Reply-To: "Hui-Hsu \(Gavin\) Tsai" From: "Hui-Hsu \(Gavin\) Tsai" To: Subject: TDDFT excited state calculation in G98 Date: Sun, 9 Sep 2001 21:49:00 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0016_01C13979.3C5F7740" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2479.0006 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2479.0006 This is a multi-part message in MIME format. ------=_NextPart_000_0016_01C13979.3C5F7740 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi CCLers, We have a question about excited state calculations by using G98W. In the excited state calculation (such as TDDFT), are the coefficients = normalized? Why is the sum of the squared coefficients not equal to 1.0 and sometimes smaller than 0.5? Here is the output of TDDFT calculations of water...=20 Excitation energies and oscillator strengths: =20 Excited State 1: Singlet-B1 8.0068 eV 154.85 nm f=3D0.0142 3 -> 14 -0.01126 5 -> 6 0.69120 5 -> 11 0.01351 This state for optimization and/or second-order correction. Total Energy, E(RPA) =3D -76.1254896781 =20 Copying the excited state density for this state as the 1-particle = RhoCI density. =20 Excited State 2: Singlet-A2 10.0437 eV 123.44 nm f=3D0.0000 5 -> 7 0.70034 5 -> 8 -0.01585 5 -> 12 0.01756 The water example shows that the sum of the squared coefficients is = about just 0.5. Should we normalize the coefficients by ourselves?=20 =20 any comment or advice is welcomed. Thanks. Gavin ------=_NextPart_000_0016_01C13979.3C5F7740 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi CCLers,
 
      We = have a=20 question about excited state calculations by using G98W.
  In = the=20 excited state calculation (such as TDDFT), are the coefficients=20 normalized?
Why is the sum of the squared coefficients not equal to=20 1.0
and sometimes smaller than 0.5?
 
    Here is the output = of TDDFT=20 calculations of water...
 
  Excitation energies and = oscillator=20 strengths:
 
  Excited State   1:  =20 Singlet-B1     8.0068 eV  154.85 nm =20 f=3D0.0142
       3 ->=20 14       =20 -0.01126
       5 -> =20 6        =20 0.69120
       5 ->=20 11         0.01351
 This = state=20 for optimization and/or second-order correction.
 Total Energy, = E(RPA)=20 =3D  -76.1254896781   
 Copying the excited = state=20 density for this state as the 1-particle RhoCI=20 density.
 
 Excited State   2:  =20 Singlet-A2    10.0437 eV  123.44 nm =20 f=3D0.0000
       5 -> =20 7        =20 0.70034
       5 -> =20 8       =20 -0.01585
       5 ->=20 12         0.01756
 
   The water example shows = that the sum=20 of the squared coefficients is about just 0.5.
 
   Should we normalize the = coefficients=20 by ourselves?
 
  any comment or advice is=20 welcomed.
 
   Thanks.
 
 =20 Gavin
------=_NextPart_000_0016_01C13979.3C5F7740-- From chemistry-request@server.ccl.net Mon Sep 10 12:52:02 2001 Received: from mercury.chem.nwu.edu (hutchisn@[129.105.116.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8AGq2M18107 for ; Mon, 10 Sep 2001 12:52:02 -0400 Received: from localhost (hutchisn@localhost) by mercury.chem.nwu.edu (8.11.3/8.11.3) with ESMTP id f8AGq2U14443 for ; Mon, 10 Sep 2001 11:52:02 -0500 (CDT) Date: Mon, 10 Sep 2001 11:52:02 -0500 (CDT) From: Geoff Hutchison X-X-Sender: To: Subject: Announce: Ghemical version 0.80 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Ghemical version 0.80 Release Announcement ------------------------------------------ Ghemical is a molecular modelling software package with GNOME and GLUT GUI front-ends and some nice 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics using MOPAC7 and MPQC for QM. Algorithms for geometry optimization (for MM and QM) and molecular dynamics (for MM) are included. Ghemical is written in C++, and offers a good framework for a generic freeware molecular modelling tool. Ghemical uses the OELib/Babel C++ framework for import and export of a wide range of chemical file formats. As the version number indicates, Ghemical is still in development, though it is already quite usable. Feedback, suggestions or contributions are very welcome. The program is made available under the GNU GPL and is free software. For more information (and screenshots) of Ghemical, see the Ghemical homepage: To download Ghemical 0.80 (current only in source form): To report bugs/suggestions for Ghemical, see the Ghemical project page: For more information on the Open Eye Scientific OELib library: -- -Geoff Hutchison Marks/Ratner Groups (847) 491-3295 Northwestern Chemistry From chemistry-request@server.ccl.net Mon Sep 10 11:39:16 2001 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8AFdFM16617 for ; Mon, 10 Sep 2001 11:39:15 -0400 Received: (from osman@localhost) by sd.accelrys.com (8.11.0/8.11.0) id f8AFfwt29538 for chemistry@ccl.net; Mon, 10 Sep 2001 08:41:58 -0700 Received: from OGUNER-LAP.accelrys.com (dhcp388.sd.accelrys.com [172.30.201.134]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id f8AFfv229435; Mon, 10 Sep 2001 08:41:57 -0700 Message-Id: <5.1.0.14.2.20010910075210.023d20b8@sparky2.sd.accelrys.com> X-Sender: osman@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 10 Sep 2001 08:35:51 -0700 To: qsar_society@accelrys.com, chemistry@ccl.net From: "Osman F. Guner" Subject: Beginnings of QSAR, CADD? Cc: osman@accelrys.com Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f8AFdGM16618 When can be considered the starting dates of QSAR or more generally Computer-Aided Drug Design? So far, there are several papers of Hansch and Fujita in the early 60's that are heavily cited for QSAR. However, are there any work earlier that can be considered as the beginning? How do you define the "beginning". If we have to draw the line somewhere, one way of defining the "beginning" is the point we have transitioned from more empirical research into "scientific" research. Hence, the early SAR papers may not necessarily qualify unless there are some statistical (or quantitative) considerations. Given the above constraints, I had a fairly clear view of the "beginnings" but after starting asking around, I am not so sure anymore. Let me share what I have found out so far, then I would like to hear from you of your opinions/suggestions. Hugo Kubinyi proposes 1964 paper by Free and Wilson (Free-Wilson model), and 1964 papers by Hansch and Fujita (Hansch model). However he also notes that a Bruice, Kharasch, and Winzler paper in 1956 with a first application of Free-Wilson type analysis. Also a paper by Zahrandic on 1960-62 with Hansch-type relationships. Yvonne Martin proposes a 1960 paper in Nature by Taylor and Wykes on MAO inhibitors. Another paper by Swett and Martin in 1963 involves Pargyline Series. Lemont Kier proposes early 1950's with articles by Coulson (1953) and by the Pullmans (1955) laying out some quantitating carcinogenic activity via valence bond and molecular orbital computations. Then I received a 17 page manuscript from Barbara and Marvin Charton's that detail the history of QSAR all the way back to 1800's. Most of the earlier work were, of course, qualitative. The quantitative SAR in which the bioactivity is mathematically related to some set of parameters came later on. The earliest mathematical formulations, according to Charton's, were Ferguson principle (started at 1939 but mostly at around 1950s) for toxicity; Hammett equation (1953); Taft equation (1956); Hansch-Fujita model (1962). So... any suggestions from here on? Are there any other references that I am missing? If not, based on the above what would be your vote for the beginnings of CADD (note I am not limiting to QSAR alone): 1- Early 50's: [Hammett, Taft, Coulson, Pullman, Ferguson] 2- Early 60's: [Hansch-Fujita; Free-Wilson; Zahrandic; Taylor] 3- Any other suggestions? I will be more than happy to organize and summarize the responses to the list. Thx...osman --- Osman F. Güner, Ph.D. Director, Lead Identification & Optimization Accelrys Inc. (858) 799-5341 osman@accelrys.com http://www.accelrys.com From chemistry-request@server.ccl.net Mon Sep 10 11:17:37 2001 Received: from hotmail.com ([64.4.31.131]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8AFHbM15916 for ; Mon, 10 Sep 2001 11:17:37 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 10 Sep 2001 08:17:31 -0700 Received: from 213.155.56.139 by pv1fd.pav1.hotmail.msn.com with HTTP; Mon, 10 Sep 2001 15:17:31 GMT X-Originating-IP: [213.155.56.139] From: "Ramin Rambod" To: CHEMISTRY@ccl.net Subject: pseudopotentials Date: Mon, 10 Sep 2001 15:17:31 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 10 Sep 2001 15:17:31.0918 (UTC) FILETIME=[B636CAE0:01C13A0B] Hi all Which computation method and program is suitable to calculate interatomic pseduopotentials for a quasimolecule such as alkali-rare gas? Can you give some references too? Thanks Ramin _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Mon Sep 10 14:42:41 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8AIgfM20383 for ; Mon, 10 Sep 2001 14:42:41 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id OAA24401; Mon, 10 Sep 2001 14:41:57 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3B9D034F.B7C88B88@cornell.edu> Date: Mon, 10 Sep 2001 14:15:43 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: CCL:Beginnings of QSAR, CADD? References: <5.1.0.14.2.20010910075210.023d20b8@sparky2.sd.accelrys.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi I suppose that you could see Chapter 3 of the book Intermolecular Interactions and Biomolecular Organization by A. J. Hopfinger. It gives a description of the development of structure and activity relationships as far as drug design goes. Cheers, Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Mon Sep 10 13:23:47 2001 Received: from mail.uni-kl.de ([131.246.137.52]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8AHNlM19009 for ; Mon, 10 Sep 2001 13:23:47 -0400 Received: from aixs1.rhrk.uni-kl.de (exim@aixs1.rhrk.uni-kl.de [131.246.137.3]) by mail.uni-kl.de (8.11.5/8.11.5) with ESMTP id f8AHNij22382 for ; Mon, 10 Sep 2001 19:23:44 +0200 (MET DST) Received: from aixd1.rhrk.uni-kl.de ([131.246.137.210] ident=exim) by aixs1.rhrk.uni-kl.de with esmtp (Exim 3.33 #2) id 15gUme-0002ca-00 for CHEMISTRY@ccl.net; Mon, 10 Sep 2001 19:23:44 +0200 Received: from gerwalin (helo=localhost) by aixd1.rhrk.uni-kl.de with local-esmtp (Exim 3.03 #5) id 15gUme-000IC2-00 for CHEMISTRY@ccl.net; Mon, 10 Sep 2001 19:23:44 +0200 Date: Mon, 10 Sep 2001 19:23:44 +0200 (MES) From: Elmar Gerwalin To: CHEMISTRY@ccl.net Subject: Q: Disk usage in G98 ( CCSD(T)) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi ! I'm trying to perform a CCSD(T) calculation with G98 on a medium sized molecule (nearly 300 basis functions), but my disk space isn't sufficient, I guess. So, how can I calculate the disk space that's really needed ? Or, in other words, could someone explain to me the meaning of this output part ?: -----snip---------------- Closed-shell transformation, MDV= 67108864 ITran=7 ISComp=1. Estimate disk for full transformation 1406403161 words. Semi-Direct transformation. ModeAB= 4 MOrb= 194 LenV= 66093971 LASXX= 278885236 LTotXX= 370408921 LenRXX= 469978396 LTotAB= 99569475 MaxLAS= 351459615 LenRXY= 0 NonZer= 657339947 LenScr= 1052103892 LnRSAI= 699314516 LnScr1= 1115065745 MaxDsk= -1 Total= 3336462549 SrtSym= T ITran= 5 JobTyp=0 Pass 1: I= 1 to 194. Complete sort for first half transformation. First half transformation complete. Begin second half transformation for I= 10. Begin second half transformation for I= 20. Begin second half transformation for I= 30. Begin second half transformation for I= 40. Begin second half transformation for I= 50. Begin second half transformation for I= 60. Begin second half transformation for I= 70. Begin second half transformation for I= 80. Begin second half transformation for I= 90. Begin second half transformation for I= 100. Erroneous write. write 49348608 instead of 55779328. ---snip---- Thank you very much for any help ! Bye Elmar ============================================================== Elmar Gerwalin , University of Kaiserslautern, Germany gerwalin@rhrk.uni-kl.de ============================================================== From chemistry-request@server.ccl.net Mon Sep 10 19:22:30 2001 Received: from deimos.email.Arizona.EDU (IDENT:root@[128.196.133.166]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8ANMTM29996 for ; Mon, 10 Sep 2001 19:22:29 -0400 Received: from demetrio.u.arizona.edu (128.196.86.129) by deimos.email.Arizona.EDU (5.1.071) id 3B99715B00030C73 for chemistry@ccl.net; Mon, 10 Sep 2001 16:22:27 -0700 Message-Id: <5.1.0.14.0.20010910161932.024c3910@deimos.email.arizona.edu> X-Sender: dasf@deimos.email.arizona.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 10 Sep 2001 16:20:21 -0700 To: chemistry@ccl.net From: Demetrio Antonio da Silva Filho Subject: quadrupol moment of the polarized molecule Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_6076867==_.ALT" --=====================_6076867==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL'ers, >I have the following question: I need to polarize a molecule applying a >quadrupolar field. I achieve that by applying point charges at a certain >distance of the molecule. Is there any program that allows me to calculate >the >quadrupol moment of the polarized molecule without considering the point >charges (i.e. The point charges should be included in the SCF cycle to >determine the charge distribution of the molecule, but they should not enter >into the quadrupolar moment that is calculated from that poit charge >distribution.)?? Thanks! Demetrio Filho --=====================_6076867==_.ALT Content-Type: text/html; charset="us-ascii" Dear CCL'ers,

I have the following question: I need to polarize a molecule applying a
quadrupolar field. I achieve that by applying point charges at a certain
distance of the molecule. Is there any program that allows me to calculate the
quadrupol moment of the polarized molecule without considering the point
charges (i.e. The point charges should be included in the SCF cycle to
determine the charge distribution of the molecule, but they should not enter
into the quadrupolar moment that is calculated from that poit charge
distribution.)??

Thanks!
Demetrio Filho
--=====================_6076867==_.ALT--