From chemistry-request@server.ccl.net Tue Jun 19 19:21:07 2001 Received: from chemsun.chem.umn.edu ([128.101.157.2]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5JNL7506483 for ; Tue, 19 Jun 2001 19:21:07 -0400 Received: (qmail 80237 invoked by uid 1121); 19 Jun 2001 18:21:07 -0500 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 19 Jun 2001 18:21:07 -0500 Date: Tue, 19 Jun 2001 18:21:07 -0500 (CDT) From: Ramkumar Rajamani To: chemistry@ccl.net Subject: Binding Free Energies Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I am looking for a database of protein-ligand complex (small ligands) and their respective experimental binding free energies. I would appreciate any help with regards to finding such information. Thanks in advance Ramkumar Rajamani From chemistry-request@server.ccl.net Tue Jun 19 23:40:37 2001 Received: from phnxpop5.phnx.uswest.net ([206.80.192.5]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5K3eb508321 for ; Tue, 19 Jun 2001 23:40:37 -0400 Received: (qmail 40712 invoked by uid 0); 20 Jun 2001 03:40:14 -0000 Received: from phnxdslgw1poolc20.phnx.uswest.net (HELO default.asu.edu) (63.229.73.20) by pop.phnx.uswest.net with SMTP; 20 Jun 2001 03:40:14 -0000 Date: Tue, 19 Jun 2001 20:42:34 -0700 Message-Id: <5.0.2.1.0.20010619204027.00a13e00@imap4.asu.edu> From: "Benjamin J Moritz" To: chemistry@ccl.net X-Sender: bmoritz@imap4.asu.edu X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Subject: Annihilation of the first spin contaminant Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_9666771==_.ALT" --=====================_9666771==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed CCL'ers Can someone help me fix a G98 problem. I keep on trying to optimize a molecule, but keep on getting the error shown below... >>>>>>>>>> Convergence criterion not met. SCF Done: E(UB+HF-LYP) = -1922.96496337 A.U. after 65 cycles Convg = 0.7322D-05 -V/T = 2.0005 S**2 = 0.7541 Annihilation of the first spin contaminant: S**2 before annihilation 0.7541, after 0.7500 Convergence failure -- run terminated. What am I doing wrong, and what do I need to fix it? Thanks for any advice. ******************************************************************************** Benjamin J. Moritz Work: 480-965-8509 College of Engineering and Applied Sciences Mailto:bmoritz@asu.edu Dept. of Chemical & Materials Engineering PO Box 876006 Tempe, AZ 85287-6006 ******************************************************************************** "Karma is justice without the satisfaction." --=====================_9666771==_.ALT Content-Type: text/html; charset="us-ascii" CCL'ers

Can someone help me fix a G98 problem.  I keep on trying to optimize a molecule, but keep on getting the error shown below...

>>>>>>>>>> Convergence criterion not met.
 SCF Done:  E(UB+HF-LYP) =  -1922.96496337     A.U. after   65 cycles
             Convg  =    0.7322D-05             -V/T =  2.0005
             S**2   =   0.7541
 Annihilation of the first spin contaminant:
 S**2 before annihilation     0.7541,   after     0.7500
 Convergence failure -- run terminated.

What am I doing wrong, and what do I need to fix it?  Thanks for any advice.


********************************************************************************
Benjamin J. Moritz Work:                                480-965-8509
College of Engineering and Applied Sciences             Mailto:bmoritz@asu.edu
Dept. of Chemical & Materials Engineering
PO Box 876006
Tempe, AZ
85287-6006
********************************************************************************


"Karma is justice without the satisfaction."
 --=====================_9666771==_.ALT-- From chemistry-request@server.ccl.net Tue Jun 19 18:36:44 2001 Received: from mail.bucknell.edu ([134.82.9.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5JMai506188 for ; Tue, 19 Jun 2001 18:36:44 -0400 Received: from WILLIAMS.bucknell.edu (williams.bucknell.edu [134.82.59.42]) by mail.bucknell.edu (8.11.4/8.11.4) with ESMTP id f5JMaaL18153; Tue, 19 Jun 2001 18:36:36 -0400 (EDT) Message-Id: <5.1.0.14.2.20010619183116.01ca6e78@mail.bucknell.edu> X-Sender: williams@mail.bucknell.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 19 Jun 2001 18:36:35 -0400 To: "S.I.Gorelsky" , "Mills, Nancy S." From: Brian Williams Subject: Re: CCL:Zindo/S vs Zindo-1 Cc: In-Reply-To: References: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed With respect to different versions of ZINDO, a reparameterized version of INDO/S (INDO/S2) useful for predicting charges and electronic transitions in molecules involving carbonyl groups was presented in Li et. al. J. Chem. Phys. 110 724(1999) (errata Li et. al. J. Chem. Phys. 111 5624 (1999). Brian Williams Chemistry Bucknell University From chemistry-request@server.ccl.net Tue Jun 19 23:37:40 2001 Received: from imc21.ex.nus.edu.sg ([137.132.14.62]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5K3bd508287 for ; Tue, 19 Jun 2001 23:37:40 -0400 Received: by imc21.ex.nus.edu.sg with Internet Mail Service (5.5.2653.19) id ; Wed, 20 Jun 2001 11:37:39 +0800 Message-ID: <30A14FB41CC5D311854D00508B5EEF020203EC01@exs23.ex.nus.edu.sg> From: Pan Jingfang To: "'chemistry@ccl.net'" Subject: reaction energy Date: Wed, 20 Jun 2001 11:37:37 +0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f5K3be508288 Dear all, To calculate the energy change of A + B ---> A···B reaction, I used the calculated energy difference of two species, DE=E(A···B)-E(AµB), E(AµB) corresponds to geometry in which A and B are well separated without any interactions. Can this reduce the basis set superposition error (BSSE) ? Thanks! Jing-Fang Pan (Mr) Institute of Materials Research and Engineering (IMRE) National University of Singapore (NUS) email: engp9078@nus.edu.sg From chemistry-request@server.ccl.net Wed Jun 20 04:45:49 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5K8jm517198 for ; Wed, 20 Jun 2001 04:45:48 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 15CdcM-0001Pc-00; Wed, 20 Jun 2001 10:45:42 +0200 Received: from vejas.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id KAA04212 for ; Wed, 20 Jun 2001 10:51:23 +0200 (GMT) Date: Tue, 19 Jun 2001 22:45:38 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <139823415.20010619224538@vaidila.vdu.lt> To: chemistry@ccl.net Subject: CCL: Genetic Algorithm routine ? In-reply-To: <5.0.2.1.0.20010619204027.00a13e00@imap4.asu.edu> References: <5.0.2.1.0.20010619204027.00a13e00@imap4.asu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, CCL'ers, It is about Genetic Algorithm (GA) implemented in AutoDock. There are "population", "max evaluations", "elitism" ,etc. Does "max evaluations" determinates the max energy evaluations needed to produce a population? Could anyone explain briefly and the essence of routine GA? Have a nice day A.Ziemys From chemistry-request@server.ccl.net Wed Jun 20 13:04:27 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5KH4R532709 for ; Wed, 20 Jun 2001 13:04:27 -0400 Received: from mail.rpi.edu (mail.rpi.edu [128.113.22.40]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id NAA03871 for ; Wed, 20 Jun 2001 13:04:25 -0400 (EDT) Received: from w18x3 (corenet-1393.dynamic.rpi.edu [128.113.170.204]) by mail.rpi.edu (8.11.3/8.11.3) with SMTP id f5KH4PR58596 for ; Wed, 20 Jun 2001 13:04:25 -0400 Message-ID: <001a01c0f9ac$0750c980$ccaa7180@dynamic.rpi.edu> From: "ADAM" To: Subject: hyperchem database Date: Wed, 20 Jun 2001 13:11:21 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0017_01C0F98A.80147000" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_0017_01C0F98A.80147000 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello all My name is Adam Stradling and I am a undergraduate researcher at = Rensellear Polytechnic Institute (RPI) in Troy NY. I was curious if anyone could direct me to a database of = hyperchem files. I need a large set of relatively common molecules. = Otherwise I will have to build them myself which could be pretty time = consuming. thanks Adam =20 ------=_NextPart_000_0017_01C0F98A.80147000 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello all
        = My name is=20 Adam Stradling and I am a undergraduate researcher at Rensellear = Polytechnic=20 Institute (RPI) in Troy NY.
         I was = curious if=20 anyone could direct me to a database of hyperchem = files. I need a=20 large set of relatively common molecules. Otherwise I will have to build = them=20 myself which could be pretty time consuming.
       =20             =    =20             =    =20             =    =20     thanks
       =20             =    =20             =    =20             =    =20        =20 Adam   
------=_NextPart_000_0017_01C0F98A.80147000-- From chemistry-request@server.ccl.net Wed Jun 20 16:03:54 2001 Received: from cermm.concordia.ca ([132.205.24.173]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5KK3r504475 for ; Wed, 20 Jun 2001 16:03:53 -0400 Received: from localhost (cyril@localhost) by cermm.concordia.ca (8.11.2/8.11.2) with ESMTP id f5KK9fi25932 for ; Wed, 20 Jun 2001 16:09:41 -0400 Date: Wed, 20 Jun 2001 16:09:41 -0400 (EDT) From: To: Subject: Seek for charge calculation comparison Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am looking for a paper (or any other reference) which would state about a comparison between different method to calculate atomic charges. More specificlly I am interested about the following methods: ESP, NBO, Mulliken, AIM Thank you for your help. -------------------------------------------------- Cyril Puel CERMM, Centre for Research in Mollecular Modelling Concordia University, Faculty of Arts and Science Departement of Chemistry and Biochemistry 1455 de Maisonneuve West Montreal, Quebec, Canada, H3G 1M8 Phone: +1-514-848-3360 Email: cyril@arsenic.concordia.ca --------------------------------------------------