From chemistry-request@server.ccl.net Wed Oct 9 04:46:48 2002 Received: from yangtze.hku.hk (IDENT:root@[147.8.148.244]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g998klJ20738 for ; Wed, 9 Oct 2002 04:46:47 -0400 Received: from localhost (lhhu@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id g998siH29578; Wed, 9 Oct 2002 16:54:44 +0800 Date: Wed, 9 Oct 2002 16:54:44 +0800 (HKT) From: Hu LiHong To: Rick Venable cc: chemistry@ccl.net Subject: Re: CCL:on calculation of protein In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I am using CHARMM to calculate the energy of protein. But the single point energy of protein and protein together with a very small molecule have so much difference (about 4000 kcal, mainly because of the electrostatic term). But if I minimize the molecule, the energy have much less difference between two molecules (only 100 kcal/mol or so). Could someone can tell me the reason about it or give me some experience on charmm minimization or reference on charmm energy explanation (can be get as soon as possible)? Thank you all, Carol From chemistry-request@server.ccl.net Wed Oct 9 10:26:40 2002 Received: from medusa.wo.utoledo.edu (IDENT:+EKhQzRx3nDxVI0SaM+pYaGDV2BKkyw5@[131.183.69.81]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g99EQeJ30938 for ; Wed, 9 Oct 2002 10:26:40 -0400 Received: from there (IDENT:pUyEY9RJEZnO2aH4EZMH0V1doK1+f8Ox@localhost.localdomain [127.0.0.1]) by medusa.wo.utoledo.edu (8.11.6/8.11.6) with SMTP id g99ETM503214 for ; Wed, 9 Oct 2002 10:29:22 -0400 Message-Id: <200210091429.g99ETM503214@medusa.wo.utoledo.edu> Content-Type: text/plain; charset="iso-8859-1" From: Venkataraman Kabaleeswaran Reply-To: vkabale@uoft02.utoledo.edu Organization: univ of toledo To: chemistry@ccl.net Subject: - lattice energy Date: Wed, 9 Oct 2002 10:29:22 -0400 X-Mailer: KMail [version 1.3.1] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit I would like to calculate the lattice energy for my protein molecule, Could someone can suggest me some free academic software for calculating lattice energy for the molecule? thank you all cheers venkataraman From chemistry-request@server.ccl.net Wed Oct 9 08:17:01 2002 Received: from atcmail.atc.tcs.co.in ([203.199.176.98]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g99CGwJ26463 for ; Wed, 9 Oct 2002 08:16:59 -0400 Received: from ATCSWETANIGAM (sweta_t.atc.tcs.co.in [172.19.40.166]) by atcmail.atc.tcs.co.in (8.11.0/8.11.0) with SMTP id g99CH9V03312 for ; Wed, 9 Oct 2002 17:47:09 +0530 Message-ID: <001f01c26f8d$bf0bd210$a62813ac@ATCSWETANIGAM> From: "sweta nigam" To: Subject: some help... Date: Wed, 9 Oct 2002 17:46:50 +0530 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001C_01C26FBB.D8B0FB40" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 This is a multi-part message in MIME format. ------=_NextPart_000_001C_01C26FBB.D8B0FB40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable hello=20 i would like to know whether we can use the partial atomic charges = assigned by j.gasteiger and m.marshil to calculate molecular orbital = energies...i mean how effective this could be? is there any formula that relates atomic charges to MO energy?hope u can = help me out...... Thanks n Regards Sweta=20 TCS ------=_NextPart_000_001C_01C26FBB.D8B0FB40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
hello
 
   i would like to know = whether we can=20 use the partial atomic charges assigned by j.gasteiger and m.marshil to=20 calculate molecular orbital energies...i mean how effective this could=20 be?
is there any formula that relates = atomic charges to=20 MO energy?hope u can help me out......
 
Thanks n Regards
Sweta
TCS
------=_NextPart_000_001C_01C26FBB.D8B0FB40-- From chemistry-request@server.ccl.net Wed Oct 9 05:56:53 2002 Received: from nikias.cc.uoa.gr ([195.134.68.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g999uqJ22457 for ; Wed, 9 Oct 2002 05:56:52 -0400 Received: from localhost (jkerkin@localhost) by nikias.cc.uoa.gr (8.9.3/8.9.3) with SMTP id MAA24068; Wed, 9 Oct 2002 12:56:40 +0300 (EET DST) Date: Wed, 9 Oct 2002 12:56:39 +0300 (EET DST) From: Ioannis Kerkines To: chminf-l@listserv.indiana.edu, chemistry@ccl.net Subject: The 2002 Nobel Prize in Chemistry 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 g999urJ22458 The Royal Swedish Academy of Sciences has just announced that the Nobel Prize in Chemistry for 2002 is awarded with one half jointly to John B. Fenn, Virginia Commonwealth University, Richmond, USA Koichi Tanaka, Shimadzu Corp., Kyoto, Japan "for the development of methods for identification and structure analyses of biological macromolecules" and the other half to: Kurt Wüthrich, Swiss Federal Institute of Technology (ETH), Zürich, Switzerland and The Scripps Research Institute, La Jolla, USA "for his development of nuclear magnetic resonance spectroscopy for determining the three-dimensional structure of biological macromolecules in solution" More info on http://www.nobel.se/chemistry/laureates/2002/press.html Regards, Ioannis Kerkines From chemistry-request@server.ccl.net Tue Oct 8 18:06:02 2002 Received: from so.sd.lionbioscience.com ([209.68.255.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g98M61J28143 for ; Tue, 8 Oct 2002 18:06:01 -0400 Received: from tempest.sd.lionbioscience.com (tempest.sd.lionbioscience.com [10.8.0.8]) by so.sd.lionbioscience.com (8.11.3/8.11.3) with ESMTP id g98M55g03540; Tue, 8 Oct 2002 15:05:09 -0700 (PDT) Received: by tempest.sd.lionbioscience.com with Internet Mail Service (5.5.2653.19) id ; Tue, 8 Oct 2002 15:05:02 -0700 Message-ID: From: Stephen Bowlus To: "'Duc Nguyen'" , chemistry@ccl.net Subject: RE: Transition state-imaginary frequency Date: Tue, 8 Oct 2002 15:04:56 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C26F16.BC91CA70" 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_01C26F16.BC91CA70 Content-Type: text/plain; charset="iso-8859-1" There are several old threads on this subject from which you can extract details ... Having a single imaginary frequency ensures that you are at a saddle point in the energy surface, which corresponds to a transition state. The significance of more than one imaginary frequency has been debated on this page. There seem to be two schools of thought: 1) if there is one large frequency (say, greater than 100 cm-1) and all others are small (say, less than 10 cm-1), this is good enough, and don't worry about it; 2) the additional imaginary frequencies may have some physical significance, so they should always be eliminated, regardless of magnitude. How to do this may depend on the software that you use. The manual for MOPAC6 has a writeup on the problem (see the section on "escaping from a hilltop"). I have found a couple of shortcuts which usually resolve the issue in MOPAC: 1) change the optimization method (e.g. from eigenvector following to Bartel's method) or 2) re-refine the structure, starting from an output file (not a restart file). The perturbation induced by the rounding/truncation in writing out the output is sometimes enough to permit further refinement. Cheers, Steve > -----Original Message----- > From: Duc Nguyen [mailto:anhduc@umich.edu] > Sent: Tuesday, October 08, 2002 2:14 PM > To: chemistry@ccl.net > Subject: CCL:Transition state-imaginary frequency > > > Dear CCLers, > > I accidentally ran by your comments in CCL.net about the transition > state should have one and only one imaginary frequency. Please suggest > me some references to read more about the matter as why it is true and > how to eliminate the other imaginary frequencies. I would greatly > appreciate your help. > > Regards, > Duc > > > -= 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 > > > > > ------_=_NextPart_001_01C26F16.BC91CA70 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RE: Transition state-imaginary frequency

There are several old threads on this subject from = which you can extract details ...

Having a single imaginary frequency ensures that you = are at a saddle point in the energy surface, which corresponds to a = transition state.

The significance of more than one imaginary frequency = has been debated on this page.  There seem to be two schools of = thought:  1) if there is one large frequency (say, greater than = 100 cm-1) and all others are small (say, less than 10 cm-1), this is = good enough, and don't worry about it; 2) the additional imaginary = frequencies may have some physical significance, so they should always = be eliminated, regardless of magnitude.

How to do this may depend on the software that you = use.  The manual for MOPAC6 has a writeup on the problem (see the = section on "escaping from a hilltop").  I have found a = couple of shortcuts which usually resolve the issue in MOPAC: 1) change = the optimization method (e.g. from eigenvector following to Bartel's = method) or 2) re-refine the structure, starting from an output file = (not a restart file).  The perturbation induced by the = rounding/truncation in writing out the output is sometimes enough to = permit further refinement.

Cheers,
Steve

> -----Original Message-----
> From: Duc Nguyen [mailto:anhduc@umich.edu]
> Sent: Tuesday, October 08, 2002 2:14 PM
> To: chemistry@ccl.net
> Subject: CCL:Transition state-imaginary = frequency
>
>
> Dear CCLers,
>
> I accidentally ran by your comments in CCL.net = about the transition
> state should have one and only one imaginary = frequency. Please suggest
> me some references to read more about the = matter as why it is true and
> how to eliminate the other imaginary = frequencies. I would greatly
> appreciate your help.
>
> Regards,
> Duc
>
>
> -=3D This is automatically added to each = message by mailing script =3D-
> 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
>
>
>
>
>

------_=_NextPart_001_01C26F16.BC91CA70-- From chemistry-request@server.ccl.net Tue Oct 8 19:52:52 2002 Received: from web13405.mail.yahoo.com ([216.136.175.63]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g98NqqJ03683 for ; Tue, 8 Oct 2002 19:52:52 -0400 Message-ID: <20021008235247.45948.qmail@web13405.mail.yahoo.com> Received: from [169.232.140.250] by web13405.mail.yahoo.com via HTTP; Tue, 08 Oct 2002 16:52:47 PDT Date: Tue, 8 Oct 2002 16:52:47 -0700 (PDT) From: eric hu Subject: amphiphilic molecule To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, I wonder if there is an efficient way to calculate the hydrophobic and/or hydrophilic end of an amphiphilic molecule either by QM or MM. Thanks. Best, -Eric __________________________________________________ Do you Yahoo!? Faith Hill - Exclusive Performances, Videos & More http://faith.yahoo.com From chemistry-request@server.ccl.net Tue Oct 8 14:17:02 2002 Received: from ramana.chem.yale.edu ([130.132.25.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g98IH2J22854 for ; Tue, 8 Oct 2002 14:17:02 -0400 Received: from localhost (mao@localhost) by ramana.chem.yale.edu (8.9.1/8.9.1) with SMTP id OAA329538 for ; Tue, 8 Oct 2002 14:16:55 -0400 (EDT) Date: Tue, 8 Oct 2002 14:16:55 -0400 (EDT) From: Fenglou Mao To: chemistry@ccl.net Subject: Can anyone introduce a free conformation search program for small molecules? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Can anyone introduce a free conformation search program for small molecules? ------------------------ Fenglou Mao Chemistry Department, Yale University, New Haven, CT. From chemistry-request@server.ccl.net Tue Oct 8 17:29:12 2002 Received: from ns.unab.cl ([200.27.72.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g98LTBJ27639 for ; Tue, 8 Oct 2002 17:29:11 -0400 Received: from quimanche (router_republica.unab.cl [200.27.72.5]) by ns.unab.cl (8.11.6/8.11.6) with SMTP id g98LReH04044; Tue, 8 Oct 2002 17:27:40 -0400 Message-ID: <002901c26f11$9e5dcdb0$0c0210ac@quimanche> From: "Ramiro Arratia" To: Cc: "Rolando Kelly" , Subject: 3rd Workshop Computational Chemistry... Date: Tue, 8 Oct 2002 17:28:17 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0026_01C26EF0.16DE77C0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 This is a multi-part message in MIME format. ------=_NextPart_000_0026_01C26EF0.16DE77C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, the complete program of the 3rd Workshop of Computational Chemistry and = Molecular Spectroscopy with the abstract pdf files are finally = available at www.unab.cl/workshop/=20 Please visit our web page. =20 Best regards, Ramiro Arratia-P=E9rez Facultad de Recursos Naturales Universidad Andr=E9s Bello Fono: (562) 661-8232 Fax: (562) 661-5679 ------=_NextPart_000_0026_01C26EF0.16DE77C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,
the complete program of the 3rd = Workshop of=20 Computational Chemistry and Molecular Spectroscopy with the  = abstract pdf=20 files are finally available at www.unab.cl/workshop/ =
 
Please visit our web page.
 
Best regards,
 
 
Ramiro Arratia-P=E9rez
Facultad de = Recursos=20 Naturales
Universidad Andr=E9s Bello
Fono:  (562)=20 661-8232
Fax:  (562) 661-5679
------=_NextPart_000_0026_01C26EF0.16DE77C0-- From chemistry-request@server.ccl.net Wed Oct 9 14:25:36 2002 Received: from haney.hbond.com ([207.137.2.252]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g99IPYJ05716 for ; Wed, 9 Oct 2002 14:25:35 -0400 Received: (from haney@localhost) by haney.hbond.com (8.9.3/8.9.3) id LAA01653; Wed, 9 Oct 2002 11:26:28 -0700 From: "Dr. David N. Haney" Message-Id: <200210091826.LAA01653@haney.hbond.com> Subject: Re: CCL:amphiphilic molecule To: erichu_linux@yahoo.com (eric hu) Date: Wed, 9 Oct 2002 11:26:26 -0700 (PDT) Cc: chemistry@ccl.net In-Reply-To: from "eric hu" at Oct 08, 2002 04:52:47 PM X-Mailer: ELM [version 2.5 PL5] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Eric: I am not sure what type of information you are looking for > from your amphiphilic molecule, but software such as HINT from eduSoft is designed precisely to calculate the hydrophobic and hydrophilic parts of molecules. The information is printed to a text file on an atom by atom basis and can be put out to a contour file to be used with various graphics programs. For more information see: http://www.edusoft-lc.com/hint/ or email me. > Hi, I wonder if there is an efficient way to calculate > the hydrophobic and/or hydrophilic end of an > amphiphilic molecule either by QM or MM. Thanks. > > Best, > -Eric -- ######### David N. Haney, Ph.D. ######### # Haney Associates Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney@hbond.com # ################# ##################### From chemistry-request@server.ccl.net Wed Oct 9 16:05:52 2002 Received: from mail.rpi.edu ([128.113.22.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g99K5qJ08606 for ; Wed, 9 Oct 2002 16:05:52 -0400 Received: from rpi.edu (omniocular-22.dynamic.rpi.edu [128.113.135.31]) by mail.rpi.edu (8.12.1/8.12.1) with ESMTP id g99K5n76361380 for ; Wed, 9 Oct 2002 16:05:49 -0400 Message-ID: <3DA48CE1.9E69C42B@rpi.edu> Date: Wed, 09 Oct 2002 16:09:05 -0400 From: "Curt M. Breneman" X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: [Fwd: grad student travel funds (CCG Excellence Awards)] Content-Type: multipart/mixed; boundary="------------D8316CE9C5A57C8F248EDF52" X-Scanned-By: MIMEDefang 2.3 (www dot roaringpenguin dot com slash mimedefang) This is a multi-part message in MIME format. --------------D8316CE9C5A57C8F248EDF52 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit --------------D8316CE9C5A57C8F248EDF52 Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: inline Return-Path: Received: from confex-32.confex.com (confex-32.confex.com [216.238.165.161]) by mail.rpi.edu (8.12.1/8.12.1) with SMTP id g99Jx576103568 for ; Wed, 9 Oct 2002 15:59:06 -0400 Received: (qmail 8881 invoked by uid 3039); 9 Oct 2002 19:58:17 -0000 Date: 9 Oct 2002 19:58:17 -0000 Message-ID: <20021009195817.8880.qmail@confex-32.confex.com> Reply-To: help@acs.org From: help@acs.org To: brenec@rpi.edu Subject: grad student travel funds (CCG Excellence Awards) X-Scanned-By: MIMEDefang 2.3 (www dot roaringpenguin dot com slash mimedefang) X-Mozilla-Status2: 00000000 The deadline for receipt of applications for the CCG Excellence Awards for graduate student travel to the New Orleans ACS national meeting (10/15/02) is rapidly approaching. Winners receive a one-year software license of CCG's MOE (Molecular Operating Environment) for their academic research groups, in addition to travel costs. Awardees are chosen on the basis of the quality and significance of the research to be presented _within the COMP Division program_ and the strength of the supporting materials. The CCG Excellence Awards were created to stimulate graduate student participation in COMP Division symposia and poster sessions at ACS National Meetings. Prior to an ACS National Meeting, an applicant must first follow the steps for OASYS abstract submission to the COMP Division program by the division's deadline (11/15/02). The following materials must also be submitted, to the COMP Treasurer (by 10/15/02 for the New Orleans meeting in Spring 2003): 1) An extended abstract of the presentation 2) A letter of recommendation from the research advisor 3) A personal statement from the applicant Information on Fall 2002 winners and deadlines for the CCG Excellence Awards for the Spring 2003 ACS meeting in New Orleans are also posted on the COMP Division web site. --Ralph Wheeler, COMP Program Chair --------------D8316CE9C5A57C8F248EDF52--