From chemistry-request@server.ccl.net Fri Jan 17 19:59:53 2003 Received: from mail.ncsa.uiuc.edu ([141.142.2.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0I0xqV30304 for ; Fri, 17 Jan 2003 19:59:52 -0500 X-Envelope-From: spamidig@ncsa.uiuc.edu X-Envelope-To: CHEMISTRY@ccl.net Received: from gozer.ncsa.uiuc.edu (roam65-237.ncsa.uiuc.edu [141.142.65.237]) by mail.ncsa.uiuc.edu (8.11.6/8.11.6) with ESMTP id h0I0xqk19108; Fri, 17 Jan 2003 18:59:52 -0600 Message-Id: <5.1.0.14.2.20030117190159.033d6c50@pop.ncsa.uiuc.edu> X-Sender: spamidig@pop.ncsa.uiuc.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 17 Jan 2003 19:02:45 -0600 To: "M. Nicklaus" , CHEMISTRY@ccl.net From: Sudhakar Pamidighantam Subject: Re: CCL:Solution Structure Databases Cc: mn1@helix.nih.gov In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Try http://www.bmrb.wisc.edu/ Sudhakar. At 01:45 PM 1/17/2003 -0500, M. Nicklaus wrote: >Does anyone know of a database, preferably publicly/freely accessible, of >solution conformations of small molecules? I guess these would typically >be NMR-determined structures. Solvent of primary interest would of course >be water; but other solvents might be of interest, too. This wouldn't >have to be a multi-hundred-thousand compound database. Still, of course, >the larger the better. > >Any useful answers will be summarized. Thanks is advance, > >Marc > >------------------------------------------------------------------------ > Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick > E-mail: mn1@helix.nih.gov Bldg 376, Rm 207 > Phone: (301) 846-5903 376 Boyles Street > Fax: (301) 846-6033 FREDERICK, MD 21702 USA > Head, Computer-Aided Drug Design MiniCore Facility > Laboratory of Medicinal Chemistry, Center for Cancer Research, > National Cancer Institute at Frederick, National Institutes of Health > http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm >------------------------------------------------------------------------ > > > > >-= 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 From chemistry-request@server.ccl.net Fri Jan 17 18:41:49 2003 Received: from aquarius.ime.eb.br ([200.20.120.44]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0HNfmV29341 for ; Fri, 17 Jan 2003 18:41:49 -0500 Received: from epq.ime.eb.br (epq.ime.eb.br [200.20.120.217]) by aquarius.ime.eb.br (8.9.1a/8.9.3) with ESMTP id VAA27212 for ; Fri, 17 Jan 2003 21:04:06 -0200 Received: from EPQ/SpoolDir by epq.ime.eb.br (Mercury 1.48); 17 Jan 03 21:41:36 -0300 Received: from SpoolDir by EPQ (Mercury 1.48); 17 Jan 03 21:41:13 -0300 Received: from usuario (200.151.33.183) by epq.ime.eb.br (Mercury 1.48); 17 Jan 03 21:41:01 -0300 Message-ID: <001201c2be7b$b42e8e40$160ffea9@usuario> From: "Teodorico Ramalho" To: Subject: Cavity size in PCM Date: Fri, 17 Jan 2003 20:56:33 -0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000F_01C2BE6A.EAD2F5A0" 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_000F_01C2BE6A.EAD2F5A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi,=20 I would like to known if anyone to have some reference about the = cavity size effect in PCM (polarizable continuum model) in calculation = with molecules in form neutral and ionized. In other words, is there = great change in cavity radii when the molecule is in its ionized form = (+1 electron) ? Thanks by help. Best regardes, Teodorico C. Ramalho =20 ------=_NextPart_000_000F_01C2BE6A.EAD2F5A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 Hi, 

   =20 I would like to known if anyone to have some reference about the cavity=20 size effect in PCM (polarizable continuum model) in calculation = with=20 molecules in form neutral and ionized. In other words, is there great = change in=20 cavity radii when the molecule is in its ionized form (+1 electron) ? = Thanks by=20 help.

 Best=20 regardes,

 Teodorico=20 C. Ramalho

 

------=_NextPart_000_000F_01C2BE6A.EAD2F5A0-- From chemistry-request@server.ccl.net Fri Jan 17 17:46:26 2003 Received: from okra.cchem.Berkeley.edu ([128.32.198.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0HMkQV28394 for ; Fri, 17 Jan 2003 17:46:26 -0500 Received: from localhost (aspuru@localhost) by okra.cchem.Berkeley.edu (8.11.0/8.11.0) with ESMTP id h0HNxup25073 for ; Fri, 17 Jan 2003 15:59:56 -0800 Date: Fri, 17 Jan 2003 15:59:56 -0800 (PST) From: Alan Aspuru-Guzik To: chemistry@ccl.net Subject: Converting Gaussians back to Slaters. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8BIT Hi to everybody, I am interested in the following problem: Given the description of a set of Gaussians for describing the 1S state for a given atom in a given molecule, how can I convert them to the best Slater-Type orbital that would reproduce the basis functions as best as possible? Shall I attempt a least squares fit? or is there a more elegant way of doing this? I know that gaussians can be derived from Slaters, but I don't know if somebody knows of a direct or semi-direct route backwards. Greetings, -- Alan Aspuru-Guzik Dios mueve al jugador, y éste, la pieza. (510)642-5911 UC Berkeley ¿Qué Dios detrás de Dios la trama empieza (925)422-8739 LLNL de polvo y tiempo y sueño y agonías? -Borges From chemistry-request@server.ccl.net Sat Jan 18 08:10:43 2003 Received: from puga.vdu.lt ([193.219.38.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0IDAgV20042 for ; Sat, 18 Jan 2003 08:10:42 -0500 Received: from amavis by puga.vdu.lt with scanned-ok for chemistry@ccl.net id 18ZskA-00057B-00; Sat, 18 Jan 2003 15:10:38 +0200 Received: from vaidila.vdu.lt ([193.219.38.52] ident=mail) by puga.vdu.lt with esmtp for chemistry@ccl.net id 18Zsk9-000572-00; Sat, 18 Jan 2003 15:10:37 +0200 Received: from vejas.vdu.lt ([193.219.38.82] helo=TYREX) by vaidila.vdu.lt with esmtp for chemistry@ccl.net id 18Zsxt-0003ci-00; Sat, 18 Jan 2003 15:24:49 +0200 Date: Sat, 18 Jan 2003 15:10:53 +0200 From: Arturas X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: Arturas Organization: SemteX X-Priority: 3 (Normal) Message-ID: <83877682.20030118151053@vaidila.vdu.lt> To: CCL Subject: GAMESS Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS snapshot-20020300 Hello, CCl'ers, Seems like I've stucked on GAMESS input file preparation: standart examples works fine. But my testsfails as there are problems reading $DATA group, although I make it IDENTICAL to examples. Tried using 'dos2unix' application, or prepare input files in Linux - no help. What the problem ???? Here is example of input and log: input: ___________________________________________________________ $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT NZVAR=0 $END $SYSTEM TIMLIM=2 MEMORY=100000 $END $STATPT OPTTOL=1.0E-5 $END $BASIS GBASIS=STO NGAUSS=2 $END $GUESS GUESS=HUCKEL $END $DATA Methylene...1-A-1 state...RHF/STO-2G C1 1 C H 1 rCH H 1 rCH 2 aHCH rCH=1.09 aHCH=110.0 $END _________________________________________________________________ log: _________________________________________________________________ EXECUTION OF GAMESS BEGUN 6:51:06 CST 18-JAN-2003 ECHO OF THE FIRST FEW INPUT CARDS - INPUT CARD> $CONTRL SCFTYP=RHF RUNTYP=OPTIMIZE COORD=ZMT NZVAR=0 $END INPUT CARD> $SYSTEM TIMLIM=2 MEMORY=100000 $END INPUT CARD> $STATPT OPTTOL=1.0E-5 $END INPUT CARD> $BASIS GBASIS=STO NGAUSS=2 $END INPUT CARD> $GUESS GUESS=HUCKEL $END INPUT CARD> $DATA INPUT CARD>Methylene...1-A-1 state...RHF/STO-2G INPUT CARD>C1 1 INPUT CARD> INPUT CARD>C INPUT CARD>H 1 rCH INPUT CARD>H 1 rCH 2 aHCH INPUT CARD> INPUT CARD>rCH=1.09 INPUT CARD>aHCH=110.0 INPUT CARD> $END 100000 WORDS OF MEMORY AVAILABLE BASIS OPTIONS ------------- GBASIS=STO IGAUSS= 2 POLAR=NONE NDFUNC= 0 DIFFSP= F NPFUNC= 0 DIFFS= F RUN TITLE --------- Methylene...1-A-1 state...RHF/STO-2G THE POINT GROUP OF THE MOLECULE IS C1 THE ORDER OF THE PRINCIPAL AXIS IS 1 A VALUE WAS GIVEN FOR A VARIABLE C NOT FOUND IN THE Z-MATRIX. A VALUE WAS GIVEN FOR A VARIABLE H NOT FOUND IN THE Z-MATRIX. A VALUE WAS GIVEN FOR A VARIABLE H NOT FOUND IN THE Z-MATRIX. A VALUE WAS GIVEN FOR A VARIABLE RCH NOT FOUND IN THE Z-MATRIX. A VALUE WAS GIVEN FOR A VARIABLE AHCH NOT FOUND IN THE Z-MATRIX. RESUBMIT AFTER FIXING YOUR Z-MATRIX ERROR(S) EXECUTION OF GAMESS TERMINATED ABNORMALLY AT 6:51:06 CST 18-JAN-2003 STEP CPU TIME = .03 TOTAL CPU TIME = .1 ( .0 MIN) TOTAL WALL CLOCK TIME= .0 SECONDS, CPU UTILIZATION IS 100.00% 0 WORDS OF DYNAMIC MEMORY USED *** ERROR TERMINATION *** IN COMPUTE PROCESS 0 DATA SERVER STATS: TOTAL DISTRIBUTED MEMORY USED (MEMDDI)= 0 MWORDS. FIRST DATA SERVER'S MAXIMUM MEMORY= 0 WORDS, CPU= .1 SECONDS. From chemistry-request@server.ccl.net Sat Jan 18 08:11:44 2003 Received: from puga.vdu.lt ([193.219.38.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0IDBhV20062 for ; Sat, 18 Jan 2003 08:11:43 -0500 Received: from amavis by puga.vdu.lt with scanned-ok for chemistry@ccl.net id 18ZslA-00058k-00; Sat, 18 Jan 2003 15:11:40 +0200 Received: from vaidila.vdu.lt ([193.219.38.52] ident=mail) by puga.vdu.lt with esmtp for chemistry@ccl.net id 18Zsl9-00058b-00; Sat, 18 Jan 2003 15:11:39 +0200 Received: from vejas.vdu.lt ([193.219.38.82] helo=TYREX) by vaidila.vdu.lt with esmtp for chemistry@ccl.net id 18Zsyt-0003cq-00; Sat, 18 Jan 2003 15:25:51 +0200 Date: Sat, 18 Jan 2003 15:11:55 +0200 From: Arturas X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: Arturas Organization: SemteX X-Priority: 3 (Normal) Message-ID: <79939731.20030118151155@vaidila.vdu.lt> To: CCL Subject: LP in AutoDock Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS snapshot-20020300 Dear CCL'ers, Have anybody tried to model lone pairs (LP) in AutoDock ? What the success ? with best regards Arturas