From chemistry-request@server.ccl.net Mon May 13 04:21:38 2002 Received: from chinon.cnrs-orleans.fr ([163.9.6.107]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4D8Lca24189 for ; Mon, 13 May 2002 04:21:38 -0400 Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.11.2/8.11.2) id g4D8Jg421361; Mon, 13 May 2002 10:19:42 +0200 X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f Sender: hinsen@chinon.cnrs-orleans.fr To: bxiong Cc: "chemistry@ccl.net" Subject: Re: CCL:the question about the normal mode analysis References: <200205130446.g4D4kR5d002709@mail.shcnc.AC.CN> From: Konrad Hinsen Date: 13 May 2002 10:19:42 +0200 In-Reply-To: <200205130446.g4D4kR5d002709@mail.shcnc.AC.CN> Message-ID: Lines: 26 User-Agent: Gnus/5.0808 (Gnus v5.8.8) Emacs/20.7 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii bxiong writes: > I want to do a normal mode analysis simulation about a protein. > 1, I think it can not include the solvent (water). Is it correct? Normal mode analysis is usually done without water, but nothing stops you from adding some or even many water molecules to the protein. > 2, how to add the effect derived from the solvent in the NMA simulation? Which effect? The presence of solvent has various effects on the dynamics of a protein, of course, but I can't think of one that would seriously affect the outcome of a normal mode analysis. Normal mode analysis is typically used to identify the slow large-amplitude motions of a protein. Their shape isn't perturbed much by the presence of solvent, and the frequencies and amplitudes from normal mode analysis are unreliable anyway. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon May 13 06:39:02 2002 Received: from mail.uni-bielefeld.de (IDENT:72@[129.70.4.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4DAd2a26742 for ; Mon, 13 May 2002 06:39:02 -0400 Received: from sorin ([129.70.59.201]) by mail.uni-bielefeld.de (Sun Internet Mail Server sims.4.0.2000.10.12.16.25.p8) with SMTP id <0GW100DCCPL03L@mail.uni-bielefeld.de> for chemistry@ccl.net; Mon, 13 May 2002 12:39:00 +0200 (MET DST) Date: Mon, 13 May 2002 12:38:30 +0200 From: Sorin Filip Subject: HOMO energy estimation To: chemistry@ccl.net Message-id: <83YUPNJISMIED9YV63ZYYX2XSNHDF96.3cdf97a6@sorin> Organization: University of Bielefeld MIME-version: 1.0 X-Mailer: Opera 6.01 build 1041 Content-type: text/plain; charset=windows-1252 Content-transfer-encoding: 7BIT X-Priority: 3 (Normal) Dear list members, Could you suggest which is the best computational method for the estimation of HOMO energies of some zinc ketone and ester enolates ? Thank you, Sorin From chemistry-request@server.ccl.net Mon May 13 06:51:06 2002 Received: from tatu2.zeon.co.jp ([210.149.8.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4DAp5a27012 for ; Mon, 13 May 2002 06:51:06 -0400 Received: from uma4.zeon.co.jp ([150.23.40.15]) by tatu2.zeon.co.jp (8.9.3/3.7W-20000321) with ESMTP id TAA20945; Mon, 13 May 2002 19:50:36 +0900 (JST) Received: from usi3.zeon.co.jp (localhost [127.0.0.1]) by uma4.zeon.co.jp (8.11.6/3.7W) with ESMTP id g4DAoau23751; Mon, 13 May 2002 19:50:36 +0900 (JST) Received: from zeon.co.jp (wadl064.lab.zeon.co.jp [150.23.1.152]) by usi3.zeon.co.jp (8.8.8/3.6W-usi3_04/21/98) with ESMTP id TAA10035; Mon, 13 May 2002 19:50:34 +0900 (JST) Message-ID: <3CDF9B9B.595674D0@zeon.co.jp> Date: Mon, 13 May 2002 19:55:23 +0900 From: Kazuo Teraishi X-Mailer: Mozilla 4.73 [ja] (Windows NT 5.0; U) X-Accept-Language: ja MIME-Version: 1.0 To: Stephen Bowlus CC: "'chemistry@ccl.net'" Subject: Re: CCL:Mopac with Cygwin References: Content-Type: multipart/alternative; boundary="------------88C183E3B067E5A0F4E8BC03" --------------88C183E3B067E5A0F4E8BC03 Content-Type: text/plain; charset=iso-2022-jp Content-Transfer-Encoding: 7bit Hi Stephen, I'm sorry for late reply. You might have already solved the problem but in case you haven't. You have to use -fno-automatic instead of -static as a g77 option. Best regards Kazuo Stephen Bowlus wrote: > I am trying to run Mopac 6 on a P3/Win2K machine under Cygwin. Set up for > 20 heavy/30 light atoms and without ESP, the program compiles with g77 with > only 2 small complaints. Test runs invoked by redirection (mopac < input > > output) end with a segmentation fault. The stackdump gives an error about a > status access violation. > > Does anyone have experience with mopac or similar packages and Cygwin or > g77? I have no idea what I need to correct to get runnable code. > > Thanks in advance, > Steve > > *************************************************************** > Stephen B. Bowlus, Ph.D. > Senior Computational Scientist > > LION bioscience, Inc. Stephen.Bowlus@lionbioscience.com > 9880 Campus Point Dr. Phone: (858) 410-6542 > San Diego, CA 92121 Fax: (858) 410-6665 > *************************************************************** > > > -- Kazuo Teraishi; Dr. Zeon Corporation --------------88C183E3B067E5A0F4E8BC03 Content-Type: text/html; charset=iso-2022-jp Content-Transfer-Encoding: 7bit Hi Stephen,

I'm sorry for late reply. You might have already solved the problem but
in case you haven't. You have to use -fno-automatic instead of -static
as a g77 option.

Best regards

Kazuo

Stephen Bowlus wrote: 

I am trying to run Mopac 6 on a P3/Win2K machine under Cygwin.  Set up for
20 heavy/30 light atoms and without ESP, the program compiles with g77 with
only 2 small complaints.  Test runs invoked by redirection (mopac < input >
output) end with a segmentation fault.  The stackdump gives an error about a
status access violation.

Does anyone have experience with mopac or similar packages and Cygwin or
g77?  I have no idea what I need to correct to get runnable code.

Thanks in advance,
Steve

***************************************************************
Stephen B. Bowlus, Ph.D.
Senior Computational Scientist    

LION bioscience, Inc.         Stephen.Bowlus@lionbioscience.com
9880 Campus Point Dr.                     Phone: (858) 410-6542
San Diego, CA 92121                         Fax: (858) 410-6665
***************************************************************

--
Kazuo Teraishi; Dr.
Zeon Corporation
  --------------88C183E3B067E5A0F4E8BC03-- From chemistry-request@server.ccl.net Mon May 13 05:38:11 2002 Received: from orionl0.ccf.auth.gr ([155.207.2.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4D9cAa25778 for ; Mon, 13 May 2002 05:38:10 -0400 Received: from chem011 (chem011.chem.auth.gr [155.207.64.94]) by orionl0.ccf.auth.gr (8.12.3/8.12.3/8.11.4) with SMTP id g4D9cGaV021294 for ; Mon, 13 May 2002 12:38:16 +0300 (EET DST) Organization: Message-ID: <002d01c1fa61$d03524c0$5e40cf9b@chem.auth.gr> From: "temper" To: Subject: NMR_MP2 Date: Mon, 13 May 2002 12:37:35 +0300 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0029_01C1FA7A.F5575520" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-Virus-Scanned: by mail.auth.gr, virus data file v4202 created May 08 2002 This is a multi-part message in MIME format. ------=_NextPart_000_0029_01C1FA7A.F5575520 Content-Type: multipart/alternative; boundary="----=_NextPart_001_002A_01C1FA7A.F5575520" ------=_NextPart_001_002A_01C1FA7A.F5575520 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable I've been trying to do a NMR computation using MP2/6-311++(2d,p)=20 with GAUSSIAN 98W A.11 but I can't. WHY?(I have an ATHLON 1.6+GHz with 512 MB memory and 30+ GB hard disk). The operating system is WINDOWS 2000. I attached the input and output files. Thanks in advance. ------=_NextPart_001_002A_01C1FA7A.F5575520 Content-Type: text/html; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable

I've been = trying to do=20 a  NMR computation using = MP2/6-311++(2d,p)=20
 with = GAUSSIAN 98W=20 A.11 but I can't.
WHY?(I have = an ATHLON=20 1.6+GHz with 512 MB memory and 30+ GB hard disk).
The = operating system is=20 WINDOWS 2000.
I attached the input and output=20 files.
Thanks in=20 advance.
------=_NextPart_001_002A_01C1FA7A.F5575520-- ------=_NextPart_000_0029_01C1FA7A.F5575520 Content-Type: application/octet-stream; name="Clbrid3(ch3).gjf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Clbrid3(ch3).gjf" %rwf=1,245mw,2,245mw,3,245mw,4,245mw,5,245mw,6,245mw,7,245mw,8,245mw,9,245mw %m=300mb #p mp2/6-311++(2d,p) nmr Clbrid3(ch3) 1 1 17 0 0.663565 -1.305419 0.424456 6 0 0.619537 0.225324 -0.682047 6 0 -0.733552 0.271480 -0.091350 6 0 1.694378 1.229467 -0.388754 6 0 -1.867021 -0.307920 -0.853607 6 0 -1.029889 1.095318 1.105708 1 0 0.634638 -0.164413 -1.696925 1 0 1.497272 2.118668 -0.998517 1 0 2.665009 0.833020 -0.689449 1 0 1.739729 1.523878 0.658294 1 0 -1.557507 -1.026257 -1.611509 1 0 -2.341305 0.542373 -1.369889 1 0 -2.624855 -0.741206 -0.199876 1 0 -0.165377 1.289914 1.736009 1 0 -1.842114 0.669888 1.695466 1 0 -1.386808 2.064235 0.720945 ------=_NextPart_000_0029_01C1FA7A.F5575520 Content-Type: application/octet-stream; name="CLBRID3(CH3).out" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="CLBRID3(CH3).out" Entering Link 1 =3D C:\G98W\l1.exe PID=3D 3348. =20 Copyright (c) 1988,1990,1992,1993,1995,1998 Gaussian, Inc. All Rights Reserved. =20 This is part of the Gaussian(R) 98 program. It is based on the Gaussian 94(TM) system (copyright 1995 Gaussian, Inc.), the Gaussian 92(TM) system (copyright 1992 Gaussian, Inc.), the Gaussian 90(TM) system (copyright 1990 Gaussian, Inc.), the Gaussian 88(TM) system (copyright 1988 Gaussian, Inc.), the Gaussian 86(TM) system (copyright 1986 Carnegie Mellon University), and the Gaussian 82(TM) system (copyright 1983 Carnegie Mellon University). Gaussian is a federally registered trademark of Gaussian, Inc. =20 This software contains proprietary and confidential information, including trade secrets, belonging to Gaussian, Inc. =20 This software is provided under written license and may be used, copied, transmitted, or stored only in accord with that written license. =20 The following legend is applicable only to US Government contracts under DFARS: =20 RESTRICTED RIGHTS LEGEND =20 Use, duplication or disclosure by the US Government is subject to restrictions as set forth in subparagraph (c)(1)(ii) of the Rights in Technical Data and Computer Software clause at DFARS 252.227-7013. =20 Gaussian, Inc. Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA =20 The following legend is applicable only to US Government contracts under FAR: =20 RESTRICTED RIGHTS LEGEND =20 Use, reproduction and disclosure by the US Government is subject to restrictions as set forth in subparagraph (c) of the Commercial Computer Software - Restricted Rights clause at FAR 52.227-19. =20 Gaussian, Inc. Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA =20 =20 --------------------------------------------------------------- Warning -- This program may not be used in any manner that competes with the business of Gaussian, Inc. or will provide assistance to any competitor of Gaussian, Inc. The licensee of this program is prohibited from giving any competitor of Gaussian, Inc. access to this program. By using this program, the user acknowledges that Gaussian, Inc. is engaged in the business of creating and licensing software in the field of computational chemistry and represents and warrants to the licensee that it is not a competitor of Gaussian, Inc. and that it will not use this program in any manner prohibited above. --------------------------------------------------------------- =20 Cite this work as: Gaussian 98, Revision A.11, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria,=20 M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr.,=20 R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam,=20 A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi,=20 V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo,=20 S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui,=20 K. Morokuma, P. Salvador, J. J. Dannenberg, D. K. Malick,=20 A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski,=20 J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko,=20 P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox,=20 T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe,=20 P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres,=20 C. Gonzalez, M. Head-Gordon, E. S. Replogle, and J. A. Pople,=20 Gaussian, Inc., Pittsburgh PA, 2001. ********************************************** Gaussian 98: x86-Win32-G98RevA.11 25-Sep-2001 27-Apr-2002=20 ********************************************** = %rwf=3D1,245mw,2,245mw,3,245mw,4,245mw,5,245mw,6,245mw,7,245mw,8,245mw,9,= 245mw %m=3D300mb ------------------------ #p mp2/6-311++(2d,p) nmr ------------------------ 1/38=3D1/1; 2/17=3D6,18=3D5,40=3D1/2; 3/5=3D4,6=3D6,7=3D1112,11=3D9,25=3D1,30=3D1/1,2,8,3; 4//1; 5/5=3D2,38=3D4/2; 8/6=3D4,8=3D1,19=3D100,23=3D2/1; 9/15=3D4,16=3D-3/6; 10/6=3D1000,13=3D1100,21=3D1,45=3D16/2; 8/6=3D4,8=3D1,19=3D100,23=3D2/11,4; 10/5=3D1,20=3D4/2; 11/12=3D2,14=3D100,16=3D11,28=3D-2/12; 6/7=3D2,8=3D2,9=3D2,10=3D2/1; 99/9=3D1/99; Leave Link 1 at Sat Apr 27 21:23:12 2002, MaxMem=3D 39321600 cpu: = 0.0 ------=_NextPart_000_0029_01C1FA7A.F5575520-- From chemistry-request@server.ccl.net Mon May 13 09:23:03 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4DDN3a29925 for ; Mon, 13 May 2002 09:23:03 -0400 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id JAA07501; Mon, 13 May 2002 09:22:59 -0400 (EDT) Sender: richard@cornell.edu Message-ID: <3CDFBE34.9E8DEA2F@cornell.edu> Date: Mon, 13 May 2002 09:23:00 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: bxiong CC: "chemistry@ccl.net" Subject: Re: CCL:the question about the normal mode analysis References: <200205130446.g4D4kR5d002709@mail.shcnc.AC.CN> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit bxiong wrote: > > Dear CCLs: > I want to do a normal mode analysis simulation about a protein. > 1, I think it can not include the solvent (water). Is it correct? Some so-called crystallographic water molecules are bound tightly enough to the protein surface that they can be seen in the electron density and included in the published pdb file. Do not believe every water molecule in a pdb file ... these positions are often highly suspect, but the small subset of ones with lowest temperature factor may be real. Also, crystallographers often do not see (or bother to identify) ions like Na, Cl etc. These are almost certainly important. The current view I have seen is that these waters and ions have a high turnover rate, but the positions spend most of their time occupied. You should take a look at the papers by Faerman and Karplus written a few years ago: FAERMAN CH, KARPLUS PA CONSENSUS PREFERRED HYDRATION SITES IN 6 FKBP12 DRUG COMPLEXES PROTEINS 23 (1): 1-11 SEP 1995 KARPLUS PA, FAERMAN C ORDERED WATER IN MACROMOLECULAR STRUCTURE CURR OPIN STRUC BIOL 4 (5): 770-776 OCT 1994 It should be possible to include these in a normal mode simulation. Would be interesting to see if they make any difference. Any large-amplitude motion of the protein, however, is likely to change the solvent environment dramatically. If you do, make sure you use a pdb file that was solved at high resolution (better than 2 Ang if possible). Better yet, if the structure was phased using signals from the halide ions or similar ... then you really know they are real. Richard Gillilan MacCHESS Cornell University From chemistry-request@server.ccl.net Mon May 13 10:44:32 2002 Received: from iris.chimfarm.unipg.it ([141.250.13.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4DEiPa32225 for ; Mon, 13 May 2002 10:44:32 -0400 Received: from apollo.chimfarm.unipg.it ([141.250.13.72] ident=mirco) by iris.chimfarm.unipg.it with esmtp (Exim 2.04 #2) id 177KHx-0002OQ-00 for chemistry@ccl.net; Mon, 13 May 2002 11:11:13 -0700 Date: Mon, 13 May 2002 15:46:27 +0200 (CEST) From: Mirco Meniconi X-Sender: mirco@localhost.localdomain To: chemistry@ccl.net Subject: request Message-ID: MIME-Version: 1.0 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 g4DEiWa32228 Dear All: I'm working on variables selection in QSAR models via GA.  I've just written a computational routine capable of carrying out such calculations.  Now I need to test my routine on very well-known datasets.   I'm looking for published datasets, however I need not only molecular structures and biological activity, but all matrixes from which one can perform chemometric analysis.   Does anybody know where I can find this? Could anybody send me any complete dataset? thanks in advance -- Mirco Meniconi PhD candidate dip. chimica e tecnologia del farmaco via del liceo 1 06100 Perugia university of Perugia (ITALY) phone: +39 075 585 5114 e-mail: mirco.me@inwind.it e-mail: mirco@unipg.it RESISTERE RESISTERE RESISTERE ... From chemistry-request@server.ccl.net Mon May 13 09:50:22 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4DDoLa30594 for ; Mon, 13 May 2002 09:50:22 -0400 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id JAA01375 for ; Mon, 13 May 2002 09:50:21 -0400 (EDT) Sender: richard@cornell.edu Message-ID: <3CDFC49D.F3DAC73B@cornell.edu> Date: Mon, 13 May 2002 09:50:21 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL: x-ray Beamtime available at Cornell Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit For those of you who may also solve structures, or are thinking about doing so, please feel free to contact us. Time slots are still available before our Summer down period (July & August). Thanks Richard Gillilan MacCHESS, Cornell ---------------------------- -- Protein Crystallography at MacCHESS -- MacCHESS, the macromolecular structure facility at the Cornell High-Energy Synchrotron Source, offers high-brightness x-ray beamtime to general academic and industrial users worldwide through a fast and simple application process. Cornell is within a day's drive of most of the Northeast as far South as the Baltimore-Washington area. Experienced staff scientists are on duty to help you and your students get the most out of your crystals. We are expanding and new users are welcome. Special experimental setups are also possible, contact the staff for details. Can't travel? Send us your crystals. We'll send you data with no collaborative/publishing obligation. o one-page, online express-mode applications for beamtime o small friendly academic environment o Ph.D. staff scientists on duty to help you o no collaborative publishing obligations o new Quantum 210 4Kx4K CCD detector with a 1 second chip readout! o BL-2 Containment for virus work o unique dual Quantum-4 CCD detector for large unit cells/high resolution (*) o 60-processor supercomputer for structure solving o support for FireWire disks, DVD (*), tape backup o multi-terabyte RAID storage o high-speed networking (gigabit internal, 100Mb out) o fast turnaround FedEX Crystallography (*) Contact MacCHESS for availability Visit our website: http://www.macchess.cornell.edu From chemistry-request@server.ccl.net Mon May 13 16:56:46 2002 Received: from mail-b.bcc.ac.uk ([144.82.100.22]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4DKujJ08925 for ; Mon, 13 May 2002 16:56:45 -0400 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Mon, 13 May 2002 21:56:44 +0100 Received: (from uccatvm@localhost) by socrates-a.ucl.ac.uk (8.11.6+Sun/8.9.3) id g4DKuhe03012; Mon, 13 May 2002 21:56:43 +0100 (BST) From: uccatvm Message-Id: <200205132056.g4DKuhe03012@socrates-a.ucl.ac.uk> Subject: counterpoise with LMP2 To: chemistry@ccl.net (CCL) Date: Mon, 13 May 2002 21:56:43 +0100 (BST) Cc: T.vanMourik@ucl.ac.uk (Tanja van Mourik) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, I am wondering what the most correct way is to do counterpoise with local MP2. In the local MP2 method originally proposed by Pulay (Chem.Phys.Lett. 100, 151, 1983), to each localised MO a subset (orbital domain) of the virtual orbitals is assigned. To calculate the interaction energy of a weakly interacting system, the orbital domains of the subsystems are first determined at large distance, and used in subsequent dimer calculations at smaller intermolecular distances (as recommended in for example Schutz et al., J. Phys. Chem. 102, 5997, 1998). Now, I assume that (to keep a true counterpoise) it is best to use the orbital domains determined at large distance for the monomer+ghost calculation. For this, one would first have to determine the domains of the monomer+ghost with the ghost at large R, and use the thus obtained orbital domains in the monomer+ghost calculation at the smaller distance. What do people think? Would this be the correct way of doing it? Of course, the BSSE is strongly reduced in LMP2, and should in principle be negligible when using an appropriate basis set. However, when using small basis sets it may not be negligible, and I would like to know the best way of doing counterpoise for these cases. Thanks in advance, Tanja -- ===================================================================== Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik@ucl.ac.uk London WC1H 0AJ, UK home: tanja@netcomuk.co.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html ===================================================================== From chemistry-request@server.ccl.net Mon May 13 12:48:54 2002 Received: from mail.nalcoexxon.com ([12.5.205.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4DGmra03639 for ; Mon, 13 May 2002 12:48:54 -0400 Received: from eslhub01.nalcoexxon.com ([192.168.52.7]) by mail.nalcoexxon.com (Lotus Domino Release 5.0.8) with ESMTP id 2002051311283742:21432 ; Mon, 13 May 2002 11:28:37 -0700 Received: from eslmal01.nalcoexxon.com ([172.22.0.117]) by eslhub01.nalcoexxon.com (Lotus Domino Release 5.0.8) with ESMTP id 2002051311412958:14074 ; Mon, 13 May 2002 11:41:29 -0500 To: chemistry@ccl.net Subject: resorcinarene conformations MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.8 June 18, 2001 Message-ID: From: "Goutam Das" Date: Mon, 13 May 2002 11:44:06 -0500 X-MIMETrack: S/MIME Sign by Notes Client on Goutam Das/US/NEEC(Release 5.0.8 |June 18, 2001) at 05/13/2002 11:46:13 AM, Serialize by Notes Client on Goutam Das/US/NEEC(Release 5.0.8 |June 18, 2001) at 05/13/2002 11:46:13 AM, Serialize complete at 05/13/2002 11:46:13 AM, S/MIME Sign failed at 05/13/2002 11:46:13 AM: The cryptographic key was not found, Serialize by Router on ESLMAL01/SRV/US/NEEC(Release 5.0.7 |March 21, 2001) at 05/13/2002 11:44:08 AM, Serialize complete at 05/13/2002 11:44:08 AM, Itemize by SMTP Server on ESLHUB01/SRV/US/NEEC(Release 5.0.8 |June 18, 2001) at 05/13/2002 11:41:29 AM, Serialize by Router on ESLHUB01/SRV/US/NEEC(Release 5.0.8 |June 18, 2001) at 05/13/2002 11:41:36 AM, Serialize complete at 05/13/2002 11:41:36 AM, Itemize by SMTP Server on ESLWEB01/SRV/US/NEEC(Release 5.0.8 |June 18, 2001) at 05/13/2002 11:28:37 AM, Serialize by Router on ESLWEB01/SRV/US/NEEC(Release 5.0.8 |June 18, 2001) at 05/13/2002 11:30:04 AM, Serialize complete at 05/13/2002 11:30:04 AM Content-Type: multipart/alternative; boundary="=_alternative 005C1EF486256BB8_=" This is a multipart message in MIME format. --=_alternative 005C1EF486256BB8_= Content-Type: text/plain; charset="us-ascii" Hello all! Could anyone please refer me to websites, etc for pdb/xyz/ or any other electronic format for the various cali[4]resorcinarene conformations. I have found sites containing info for calix[4]arenes but none for the resorcinarenes. Thanx in anticipation Goutam Das, Ph.D Senior Research Chemist ONDEO_NALCO Energy Services 7705 Hwy 90 A Sugar Land, TX 77478 # 281.263.7919 gdas@ondeo-nes.com --=_alternative 005C1EF486256BB8_= Content-Type: text/html; charset="us-ascii"
Hello all!


Could anyone  please refer me to websites, etc for pdb/xyz/ or any other electronic format for the various cali[4]resorcinarene conformations.  I have found sites containing info for calix[4]arenes but none for the resorcinarenes.

Thanx in anticipation

Goutam Das, Ph.D
Senior Research Chemist
ONDEO_NALCO Energy Services
7705 Hwy 90 A
Sugar Land, TX 77478
# 281.263.7919
gdas@ondeo-nes.com --=_alternative 005C1EF486256BB8_=-- From chemistry-request@server.ccl.net Mon May 13 14:51:58 2002 Received: from org.chem.msu.su ([158.250.32.94]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4DIpvJ05981 for ; Mon, 13 May 2002 14:51:57 -0400 Received: from orgqsar10 ([158.250.48.109]) by org.chem.msu.su (8.9.3/8.9.3) with SMTP id WAA02044 for ; Mon, 13 May 2002 22:51:56 +0400 (MSD) Message-ID: <002101c1faaf$11a48520$6d30fa9e@chem.msu.su> From: "Tikhonova Irina" To: Subject: Problem with ligands containing halogens in AutoDock, Version 3.0.3 Date: Mon, 13 May 2002 22:50:35 +0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001E_01C1FAD0.9840A700" 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_001E_01C1FAD0.9840A700 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: quoted-printable Dear AutoDock users, I have a problem with ligands containing halogens.=20 For example, for ligand with F atom it forms F-map in dpf-step but = doesn't calculate F-map in the following step (autogrid) and = autodock-step can't do nothing because of absence F-map. In the case of Br atom, it doesn't form BR-map but autodock-step gives " = Atom type error, cant't find type for "BR" in type list "CNOH" ". What I should do? Thank you in advance. Irina Tikhonova Division of Organic Chemistry Department of Chemistry Moscow State University Lenin Hills, Moscow Russia 119899 Tel: +7-095-939 35 57 Fax: +7-095-939 02 90 e-mail: tikiri@org.chem.msu.su ------=_NextPart_000_001E_01C1FAD0.9840A700 Content-Type: text/html; charset="koi8-r" Content-Transfer-Encoding: quoted-printable
Dear AutoDock users,
I have a problem with ligands = containing halogens.=20
For example, for ligand with F = atom  it forms=20 F-map in dpf-step but doesn't calculate F-map in the following=20 step (autogrid) and autodock-step can't do nothing because of = absence=20 F-map.
In the case of Br atom, it doesn't form = BR-map but=20 autodock-step gives " Atom type error, cant't find type for "BR" in type = list=20 "CNOH" ".
What I should do?
Thank you in advance.
 
 

Irina=20 Tikhonova

Division of Organic = Chemistry

Department of=20 Chemistry

Moscow State=20 University

Lenin Hills,=20 Moscow

Russia=20 119899

Tel: +7-095-939 35=20 57

Fax: +7-095-939 02=20 90

e-mail: tikiri@org.chem.msu.su


------=_NextPart_000_001E_01C1FAD0.9840A700-- From chemistry-request@server.ccl.net Mon May 13 12:23:00 2002 Received: from mserver2.gmu.edu ([129.174.0.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4DGN0a03003 for ; Mon, 13 May 2002 12:23:00 -0400 Received: from gmu.edu ([129.174.103.44]) by mserver2.gmu.edu (Netscape Messaging Server 4.15) with ESMTP id GW25IA00.RH0; Mon, 13 May 2002 12:22:58 -0400 Message-ID: <3CDFE8F3.E1774296@gmu.edu> Date: Mon, 13 May 2002 12:25:23 -0400 From: "Glenda Wilson" X-Mailer: Mozilla 4.7 [en] (Win98; U) X-Accept-Language: en,pdf MIME-Version: 1.0 To: chemistry@ccl.net Subject: Computational Protein Structure Analysis Workshop (May 24, 2002) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit George Mason University School of Computational Sciences Computational Protein Structure Analysis and Structural Genomics One-day workshop May 24, 2002 This intensive workshop is designed for scientists with limited prior experience in computational molecular biology. The course covers theoretical approaches, techniques and computational tools for protein structure analysis, classification, and prediction. The workshop will consist of lectures and hands-on computer laboratory sessions. The workshop provides an overview of methods and algorithms for protein structure analysis. Students will acquire knowledge of fundamental principles as well as practical skills necessary to use modern computational tools for protein structure analysis. The topics include protein geometry and topology, 3D structure and structure classification databases, knowledge-based protein modeling, and structural genomics. Instructor: Iosif Vaisman, Associate Professor of Bioinformatics, School of Computational Sciences, George Mason University The course will be taught using state-of-the-art training facilities at the Prince William Campus of George Mason University (in the Washington, DC area). For more information see http://www.ib3.gmu.edu/educate/proteinstructure or email Glenda Wilson (gwilson1@gmu.edu). Tuition fee - $380. Discounts for multiple participants from the same organization are available. Continuing education credits might be available. Participation is limited to 20 people. You may apply online at http://ib3.gmu.edu/educate/registration/Registration.htm GMU workshops are intensive hands-on courses designed to teach cutting edge methods in molecular biology, biotechnology and bioinformatics. Several courses on different topics are offered each year. All participants benefit from in-depth interaction with instructors. To learn more about the other workshops visit the workshops web site at http://www.ib3.gmu.edu/workshops Glenda Wilson Professional Training and Education From chemistry-request@server.ccl.net Mon May 13 17:00:10 2002 Received: from iris.iupui.edu ([134.68.220.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4DL0AJ09056 for ; Mon, 13 May 2002 17:00:10 -0400 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by iris.iupui.edu (8.9.3/8.9.3/IUPUIPO.20020221) with SMTP id QAA27029 for ; Mon, 13 May 2002 16:00:10 -0500 (EST) Message-ID: Date: 13 May 2002 16:10:14 -0500 From: "Boyd" Subject: Gordon Conference program To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Dear Colleagues, Here is the program for the 9th biennial Gordon Research Conference on Computational Chemistry, Colby-Sawyer College, New London, New Hampshire, June 30-July 5, 2002. For more information and application, please see http://www.grc.uri.edu/ For ALL other questions, please direct them to: Dr. Bernard Brooks, Chair Dr. William Swope, Vice-Chair Thanks, Don Donald B. Boyd, Ph.D. Councilor, Gordon Research Conferences on Computational Chemistry http://chem.iupui.edu/rcc/grccc.html Editor, Reviews in Computational Chemistry Indiana University-Purdue University at Indianapolis -------------------------------------------------------- Program for the 2002 Computational Chemistry Gordon Research Conference Chair: Bernard Brooks (National Institutes of Health) Co-Chair: William Swope (IBM) -------------------------------------------------------- Opening Session -------------------------------------------------------- Sunday PM Session chair: Donald Boyd (IUPUI) Sharon Hammes-Schiffer (Pennsylvania State University) " Hybrid Quantum-Classical Molecular Dynamics of Proton and Hydride Transfer Reactions in Enzymes" Sharon Glotzer (University of Michigan) "Simulations of Spatially Heterogeneous Dynamics in Supercooled Liquids" -------------------------------------------------------- Session in remembrance of Michael Zerner -------------------------------------------------------- Monday AM Session chair: John McKelvey (McKelvey Computational Chemistry) Walter Thiel (Max-Planck-Institut fuer Kohlenforschung) "Semiempirical methods for electronically excited states" Sergei Tretiak (Los Alamos National Laboratory ) "Semiempirical/RPA approaches for excited state molecular electronic structures" Stefan Grimme (Universitaet Muenster) "Theoretical Electronic Spectroscopy for Large Molecules with ab initio Methods" Kichisuki Nishimoto (Osaka City University) "Quantum Theoretical Study of Electronic Spectra of Organic Colorants" -------------------------------------------------------- Session on quantum mechanics and QM/MM methods -------------------------------------------------------- Monday PM Session chair: Richard Friesner (Columbia University) David Sherrill (Georgia Tech) "Using linear R12 methods to obtain the ab initio limit for pi-pi interactions". Qiang Cui (University of Wisconsin, Madison) "Theoretical studies of catalysis and conformational transition in proteins" -------------------------------------------------------- Session in remembrance of Peter Kollman -------------------------------------------------------- Tuesday AM Session chair: David Case (The Scripps Research Institute) David Case (The Scripps Research Institute) "New force fields in Amber 7: polarizabilties, lone pairs, continuum solvents and generalized parameters" Carlos Simmerllingng (SUNY at Stony Brook) TBA Thomas Cheatham, III (University of Utah) "Atomistic insight into nucleic acid structure, dynamics and energetics" David Pearlman (Vertex Pharmaceuticals) "Good enough? Qualitative alternatives to free energy calculations." -------------------------------------------------------- Session on drug design -------------------------------------------------------- Tuesday PM Session chair: Terry Stouch (Bristol-Myers Squibb Pharmaceutical Research Institute) Gennady Verkhivker (Agouron Pharmaceuticals) "Structure, energetics, dynamics and design of intermolecular interfaces : The Binding Energy landscape perspective." Dimitris Agrafiotis (3-Dimensional Pharmaceuticals) TBA Richard Friesner (Columbia University) "Computational Methods for Structure Based Drug Design" -------------------------------------------------------- Session on advances in simulation methods -------------------------------------------------------- Wednesday AM&PM Session chair: Wilfred van Gunsteren (ETH) Wilfred van Gunsteren (ETH) TBA Jay Ponder (Washington Univ. School of Medicine) "Construction and Application of a General-Purpose Polarizable Force Field" Gerhard Hummer (National Institutes of Health) "Carbon nanotubes as molecular channels" Mark Tuckerman (New York University) "A novel variable transformation approach for enhancing conformational sampling in complex systems" Douglas Tobias (University of California, Irvine) "Ab Initio Molecular Dynamics Studies of Electronic Polarization Effects in Biological Molecules" Selected poster presentations (2) -------------------------------------------------------- Session on simulating large systems -------------------------------------------------------- Thursday AM&PM Session chair: William Jorgensen (Yale University) William Jorgensen (Yale University) TBA Carol Post (Purdue University) "Antiviral Activity of Human Rhinovirus, a Molecular Dynamics Study" Siewert-Jan Marrink (University of Groningen) TBA Emad Tajkhorshid (University of Illinois at Urbana-Champaign) "Computational Chemistry for Membrane Channels" Thomas Woolf (Johns Hopkins University) "Probing alchemical transitions with non-equilibrium thermodynamics" Chung F. Wong (HHMI/UCSD) "Computer-aided design of specific protein kinase inhibitors" Selected poster presentation From chemistry-request@server.ccl.net Mon May 13 16:29:39 2002 Received: from gull.prod.itd.earthlink.net ([207.217.120.84]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4DKTZJ08110 for ; Mon, 13 May 2002 16:29:38 -0400 Received: from user-2ivftha.dialup.mindspring.com ([165.247.246.42] helo=uci.edu) by gull.prod.itd.earthlink.net with esmtp (Exim 3.33 #2) id 177MRq-00045G-00 for chemistry@ccl.net; Mon, 13 May 2002 13:29:34 -0700 Sender: heffron@ccl.net Message-ID: <3CE0214E.DC99FA72@uci.edu> Date: Mon, 13 May 2002 13:25:50 -0700 From: Susan Heffron Organization: University of California, Irvine X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: rotatable bonds question, using autodock Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi. Forgive my basic chemistry questions... I am planning to dock various small molecules to a protein using Autodock. Some of my small molecules have structures such that I am not sure how to assign certain bonds... rotatable or not (e.g., partial double-bond character or not). Specifically, my questions are: 1. In a structure with -N-C-N- would there be partial double-bond " O character to both C-N bonds, or only one (like a peptide bond)? 2. In a structure with -N-C-N- would there be a partial double-bond " S character to the N-C and C=S bonds, or not? Thanks in advance for your help. Susan -- ------------------------------------------------------------------ Susan Heffron Dept. of Physiology and Biophysics University of California, Irvine Irvine, CA 92697-4560 U.S.A. phone: (949) 824-4625 FAX: (949) 824-8540 ------------------------------------------------------------------