From chemistry-request@server.ccl.net Tue May 28 13:41:02 2002 Received: from igc.phys.chem.ethz.ch ([129.132.218.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4SHf1C22303 for ; Tue, 28 May 2002 13:41:01 -0400 Received: from igc.phys.chem.ethz.ch (humagne [129.132.218.162]) by igc.phys.chem.ethz.ch (8.11.4/8.11.4) with ESMTP id g4SBVBx23909 for ; Tue, 28 May 2002 13:31:15 +0200 (MEST) Sender: portmann@igc.phys.chem.ethz.ch Message-ID: <3CF36A7F.186C2FDD@igc.phys.chem.ethz.ch> Date: Tue, 28 May 2002 13:31:11 +0200 From: Stefan Portmann X-Mailer: Mozilla 4.76 [en] (X11; U; SunOS 5.8 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: WATOC'02: Last Call for Contributions! Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Madam or Sir 6th WORLD CONGRESS OF THEORETICALLY ORIENTED CHEMISTS (WATOC'02) August 4-9, 2002, Palazzo dei Congressi, Lugano, Switzerland More than 100 talks and over 400 poster presentations in Theory, Computation and Information Science in Chemistry, Biochemistry and Materials Science. Don't miss this great event! Last Call for Contributions: Please submit an abstract for your contribution until the end of May using the online form at http://www.watoc02.ch (Deadline: May 31, 2002). WATOC'02 special issue of THEOCHEM: We are pleased to announce that Elsevier will publish a WATOC'02 special issue of THEOCHEM to appear in Spring 2003. You are therefore invited to submit a full paper. Information and Registration: http://www.watoc02.ch. Registrations are accepted until June 14, 2002. We are looking forward to see you in Lugano. Hans Peter Luethi and Stefan Portmann ETH Zurich From chemistry-request@server.ccl.net Tue May 28 14:06:14 2002 Received: from myrtle.rtpnc.epa.gov ([134.67.208.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4SI6EC23258 for ; Tue, 28 May 2002 14:06:14 -0400 Received: from epahub11.rtp.epa.gov (epahub11.rtp.epa.gov [134.67.213.52]) by epamail.epa.gov (PMDF V5.2-32 #42055) with ESMTP id <0GWT004BPOVPES@epamail.epa.gov> for chemistry@ccl.net; Tue, 28 May 2002 09:16:37 -0400 (EDT) Date: Tue, 28 May 2002 09:16:51 -0400 From: Moudgal.Chandrika@epamail.epa.gov Subject: RE: Complete citations To: chemistry@ccl.net Message-id: MIME-version: 1.0 X-Mailer: Lotus Notes Release 5.0.6a January 17, 2001 Content-type: text/plain; charset=us-ascii X-MIMETrack: Serialize by Router on EPAHUB11/USEPA/US(Release 5.0.9a |January 7, 2002) at 05/28/2002 09:16:54 AM Hello, I am looking for complete citations to work published by the Russian chemist Borodin (1858) who was one of the few to first discover the relationship between toxicological properties and chemical make up. I would also like a complete citation for the "five rules of thumb" by Chris Lapinski. My search at the library in house, the public library and the university library has proven futile. Any help from members will be much appreciated. Thanks all in advance for your time and help. Sincerely, Chandrika Chandrika J. Moudgal National Center for Environmental Assessment, US EPA 26 W. Martin Luther King Dr., ML 117 Cincinnati, OH 45268 Phone: 513-569-7078 Fax: 513-569-7475 e-mail: moudgal.chandrika@epa.gov From chemistry-request@server.ccl.net Tue May 28 13:42:08 2002 Received: from mail.takas.lt ([212.59.31.78]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4SHg7C22367 for ; Tue, 28 May 2002 13:42:08 -0400 Received: from olegas ([212.59.14.195]) by mail.takas.lt with Microsoft SMTPSVC(5.0.2195.2966); Tue, 28 May 2002 15:30:38 +0200 Message-ID: <000e01c2064c$94fdb010$c30e3bd4@olegas> From: "Olegas Eicher-Lorka" To: Subject: TX90- Where? Date: Tue, 28 May 2002 15:35:47 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000B_01C2065D.56E245F0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-OriginalArrivalTime: 28 May 2002 13:30:38.0573 (UTC) FILETIME=[DAF701D0:01C2064B] This is a multi-part message in MIME format. ------=_NextPart_000_000B_01C2065D.56E245F0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All, How do I get hold of a copy of TX90, preferably for a PC, although code = is good? Thanks. Olegas ------=_NextPart_000_000B_01C2065D.56E245F0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear All,
 
How do I get hold of a copy of TX90, = preferably for=20 a PC, although code is good?
 
Thanks.
 
Olegas
------=_NextPart_000_000B_01C2065D.56E245F0-- From chemistry-request@server.ccl.net Tue May 28 16:28:50 2002 Received: from zeus.biomol.uci.edu (root@[128.195.179.142]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4SKSoC26431 for ; Tue, 28 May 2002 16:28:50 -0400 Received: from uci.edu (heffron@athena.biomol.uci.edu [128.195.179.141]) by zeus.biomol.uci.edu (8.9.3/) with ESMTP id UAA1219497 for ; Tue, 28 May 2002 20:28:46 GMT Sender: heffron@uci.edu Message-ID: <3CF3E87D.3F477BD1@uci.edu> Date: Tue, 28 May 2002 13:28:45 -0700 From: Susan Heffron Reply-To: sheffron@uci.edu Organization: UCI X-Mailer: Mozilla 4.75 [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: charged ligand for autodock Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Autodock users, What is the best way to assign charges to an ionized ligand for docking with Autodock? I have been using AutoDockTools to add Gasteiger charges to my ligands, and then editing the pdbq file to remove a hydrogen and add a -1 charge to the nitrogen that is ionized. But I'm sure that isn't an accurate way to do it. If I remove the hydrogen before feeding the coordinates to ADT, the charges are different, but the overall charge is 0.0 (neutral), which isn't what I want. Is there any way to tell ADT that a ligand should be charged? If not, how should I calculate, or approximate, the partial charges on my ionized ligand? Susan O " P.S. The group on the ligand that is ionized is -S-NH2 " O -- ------------------------------------------------------------------ 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 ------------------------------------------------------------------ From chemistry-request@server.ccl.net Tue May 28 13:42:07 2002 Received: from mail.takas.lt ([212.59.31.78]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4SHg6C22362 for ; Tue, 28 May 2002 13:42:07 -0400 Received: from olegas ([212.59.14.195]) by mail.takas.lt with Microsoft SMTPSVC(5.0.2195.2966); Tue, 28 May 2002 14:19:29 +0200 Message-ID: <000101c20642$a4a17c90$c30e3bd4@olegas> From: "Olegas Eicher-Lorka" To: Subject: G98W BSSE: SUMMARY Date: Tue, 28 May 2002 10:22:53 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_002E_01C20631.A03112D0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-OriginalArrivalTime: 28 May 2002 12:19:29.0639 (UTC) FILETIME=[EA7B5F70:01C20641] This is a multi-part message in MIME format. ------=_NextPart_000_002E_01C20631.A03112D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, Many thanks for all of the replies for our orginal question: In the "standard" BSSE equation (for a dimer AB): =20 BSSE(AB) =3D E(AB)^AB - E(A)^A - E(B)^B + [E(A')^A - E(A')^AB + E(B)^B - = E(B)^AB] =20 I've got most of the parameters, but how in G98W do I calculate E(A)^AB = and E(B)^AB, i.e. the energy of the monomer units in terms of the dimer = basis set. Sam Abrash wrote: "You replace the other molecule's atoms with ghost atoms that are still = assigned the basis functions of the other molecule and then you do the = calculation. It's the counterpoise method." I actually did this originally, but I obtained "strange" results, which = I thought meant that I had done something wrong. It turns out that the keyword to use is MASSAGE: Wolfgang Roth wrote: "to calculate E(A)^AB and E(B)^AB usually the atomic charge of the non intesting atoms , e.g. B resp. B, is set to zero. Thus, the basic = functions of these atoms are still present. In Gaussian, the massage keyword is = used" But many thanks go to Tanja van Mourik who gave me an excellent = reference list: "With Gaussian, the keyword Massage has to be used for counterpoise=20 corrections (assuming it's the same for G98 and G98W). Have a look at = the=20 Gaussian manual: http://www.gaussian.com/00000452.htm. There is an example there as well. However, don't believe the sentence about counterpoise being only a crude estimate, have a look at the=20 following papers to learn more about BSSE and Counterpoise: - F.B. van Duijneveldt, J.G.C.M. van Duijneveldt-van de Rijdt, and J.H. van Lenthe, Chem. Rev. 94, 1873, 1994 (on counterpoise theory) - S. Simon, M. Duran, J.J. Dannenberg, J. Chem. Phys. 105, 1996 (on geometry optimizations on BSSE-corrected potential energy = surfaces). - F.B. van Duijneveldt, "Basis Superposition Error" in "Molecular Interactions" S. Scheiner (ed.), Wiley (1997) - T. van Mourik, A.K. Wilson, K.A. Peterson, D.E. Woon, T.H. Dunning, = Jr., Adv. Quant. Chem. 31, 105, 1999 (showing BSSE effects on interaction energies, distances, and frequencies)." Ta very much Tanja! Olegas ------=_NextPart_000_002E_01C20631.A03112D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers,
 
Many thanks for all of the replies = for our=20 orginal question:
 
In the "standard" BSSE equation (for a = dimer=20 AB):
 
BSSE(AB) =3D E(AB)^AB - E(A)^A - E(B)^B + [E(A')^A - = E(A')^AB +=20 E(B)^B - E(B)^AB]
 
I've got most of the parameters, but how = in G98W=20 do I calculate E(A)^AB and E(B)^AB, i.e. the energy of the monomer units = in=20 terms of the dimer basis set.
 
Sam Abrash wrote:
 
"You replace=20 the other molecule's atoms with ghost atoms that are still assigned the = basis=20 functions of the other molecule and then you do the calculation.  = It's the=20 counterpoise method."
 
I actually did this originally, but I = obtained=20 "strange" results, which I thought meant that I had done something=20 wrong.
 
It turns out that the keyword to use is = MASSAGE:
 
Wolfgang Roth wrote:
 
"to calculate=20 E(A)^AB and E(B)^AB usually the atomic charge of the non
intesting = atoms ,=20 e.g. B resp. B, is set to zero. Thus, the basic functions
of these = atoms are=20 still present. In Gaussian, the massage keyword is = used"
 
But many thanks go to Tanja van Mourik = who gave me=20 an excellent reference list:
 
"With Gaussian,=20 the keyword Massage has to be used for counterpoise
corrections = (assuming=20 it's the same for G98 and G98W).  Have a look at the
Gaussian = manual:=20 http://www.gaussian.com/00000452.htm.
There is an example there as = well. However,=20 don't believe the sentence
about counterpoise being only a crude = estimate,=20 have a look at the
following papers to learn more about BSSE and=20 Counterpoise:

-  F.B. van Duijneveldt, J.G.C.M. van = Duijneveldt-van=20 de Rijdt, and
   J.H. van Lenthe, Chem. Rev. 94, 1873, 1994 = (on=20 counterpoise theory)

-  S. Simon, M. Duran, J.J. Dannenberg, = J.=20 Chem. Phys. 105, 1996
   (on geometry optimizations on=20 BSSE-corrected potential energy surfaces).

-  F.B. van = Duijneveldt,=20 "Basis Superposition Error"
   in "Molecular Interactions" = S.=20 Scheiner (ed.), Wiley (1997)

-  T. van Mourik, A.K. Wilson, = K.A.=20 Peterson, D.E. Woon, T.H. Dunning, Jr.,
   Adv. Quant. = Chem. 31,=20 105, 1999 (showing BSSE effects on interaction
   energies, = distances, and frequencies)."
 
Ta very much Tanja!
 
Olegas


 
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