g98 and IR-spectra/ Addition to summary

From chemistry-request@server.ccl.net Wed Sep 25 16:38:03 2002 Received: from copland.udel.edu ([128.175.13.92]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8PKc3a07155 for ; Wed, 25 Sep 2002 16:38:03 -0400 Received: from [128.175.138.90] ([128.175.138.90]) by copland.udel.edu (8.9.3/8.9.3) with ESMTP id QAA15929 for ; Wed, 25 Sep 2002 16:38:03 -0400 (EDT) Message-Id: <200209252038.QAA15929@copland.udel.edu> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Wed, 25 Sep 2002 16:17:31 -0400 Subject: g98 and IR-spectra/ Addition to summary From: "Olga Dmitrenko" To: chemistry@ccl.net Mime-version: 1.0 X-Priority: 3 Content-type: multipart/alternative; boundary="MS_Mac_OE_3115815451_1190634_MIME_Part" > 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. --MS_Mac_OE_3115815451_1190634_MIME_Part Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Hi, Here is an addition to my previous summary on the question about data for IR-spectra from g98 output file: * I've got the msg from M=E1rio Ramos after I sammerized. But I really appreciate it, thanks. Mario suggests to generate the file freqchk.scr with the keyword freqchk (number of checkpoint). Then, use emacs to create a macro that copy these numbers and put in a line on another file. *I've got Ecxel file with macros and instructions from Roma Oakes . It work= s nicely. Thanks. * I also tested recent suggestion of Laurence Cuffe. I works nicely as well= . Thanks. It uses the cut and paste commands and works for me in redhat 7.2 and Digital/compaq64 unix. The cut command might have to be replaced in a BSD unix by something based on "colrm" As before we assume the output file is test.log this time and we will create five intermediate files testF.txt, testI.txt A.txt, B.txt and C.txt. C.txt is the new output file. It will have two columns of data in it, the first frequencies and the second intensities. The following three lines makes this happen, in case my mailer reformats it the first two lines start with cut, the last line with paste and they were used in the cshell csh. grep Frequencies test.log > testF.txt; grep Inten test.log > testI.txt cut -c18-26 testF.txt > A.txt; cut -c41-49 testF.txt >> A.txt; cut - c64-72 testF.txt >> A.txt; cut -c18-26 testI.txt > B.txt; cut -c41-49 testI.txt >> B.txt; cut -c64- 72 testI.txt >> B.txt; paste A.txt B.txt > C.txt; I am very grateful to all of you and hope that my summaries will be of help to others. Bests, Olga --MS_Mac_OE_3115815451_1190634_MIME_Part Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable g98 and IR-spectra/ Addition to summary Hi,

Here is an addition to my previous summary on the question about
data for IR-spectra from g98 output file:

* I've got the msg from M=E1rio Ramos after I sammerized. But I really apprec= iate it, thanks.
Mario suggests to generate the file freqchk.scr with the keyword
freqchk (number of checkpoint). Then, use emacs to create a macro that copy= these
numbers and put in a line on another file.

*I've got Ecxel file with macros and instructions from Roma Oakes . It work= s nicely. Thanks.

* I also tested recent suggestion of Laurence Cuffe. I works nicely as well= . Thanks.

It uses the cut and paste commands and works for me in redhat 7.2 and Digital/compaq64 unix. The cut command might have to be replaced in a BSD unix by something based on "colrm" As before we assume the output file is test.log this time and we will create five intermediate files testF.txt, testI.txt A.txt, B.txt and <= BR> C.txt. C.txt is the new output file. It will have two columns of data in it, the first frequencies and the second intensities. The following three lines makes this happen, in case my mailer reformats it the first two lines start with cut, the last line with paste <= BR> and they were used in the cshell csh. grep Frequencies test.log > testF.txt; grep Inten test.log > testI.tx= t cut -c18-26 testF.txt > A.txt; cut -c41-49 testF.txt >> A.txt; cut= - c64-72 testF.txt >> A.txt; cut -c18-26 testI.txt > B.txt; cut -c41-49 testI.txt >> B.txt; cut= -c64- 72 testI.txt >> B.txt; paste A.txt B.txt > C.txt;I am very grateful to all of you and hope that my summaries will be of= help to others.
Bests,
Olga --MS_Mac_OE_3115815451_1190634_MIME_Part-- From chemistry-request@server.ccl.net Thu Sep 26 04:02:35 2002 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8Q82Ya28311 for ; Thu, 26 Sep 2002 04:02:34 -0400 Received: from mach.vub.ac.be (mach.ulb.ac.be [164.15.128.3]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id KAA19177; Thu, 26 Sep 2002 10:00:17 +0200 (MEST) for From: cbiot@ulb.ac.be Received: from ulb.ac.be (chimorg-pc5.ulb.ac.be [164.15.61.104]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id KAA09208; Thu, 26 Sep 2002 10:02:27 +0200 (MET DST) for Sender: christophe@mach.vub.ac.be Message-ID: <3D92C014.8C850791@ulb.ac.be> Date: Thu, 26 Sep 2002 10:06:44 +0200 Organization: ULB X-Mailer: Mozilla 4.77 [fr] (X11; U; Linux 2.4.4-4GB i686) X-Accept-Language: en MIME-Version: 1.0 To: Liste CCL Subject: solvation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Since some years, we studied non-covalent interactions (especially H-bond, stacking and cation pi) at the interface between protein and nucleobase (DNA or ligand). And performed, ab initio quantum mechanics energy calculations . Actually, we focussed on cation-pi interactions between a charged amino acid (such as Arg or Lys) and an aromatic ring of nucleic acid base (such as Adenine). However, until today, most of the calculations have been performed in vacuum and the transposition of vacuum energy values to energy values in water can entail modifications in the energy ranking. Recently, I try to use the polarizable continuum model (PCM) available in Gaussian 98 Revision A.7, but surprising results have been obtained (the interaction ernergie is positiv). I have also used the mixed continuum-discrete solvation methods (ref JACS 2002 Mennucci). But severe discontinuities are observed along the path (physically unreasonable ???). The SM module included in Spartan gave also strange results.... ====I would like to know if someone has already used those models for studying non convalent interactions.=== ...and could help me ??? best & take care Biot C. -- ******************************************************* Dr. BIOT Christophe Ingenierie Biomoleculaire, CP 165/64 Universite Libre de Bruxelles 50, Av. F. Roosevelt B-1050 Bruxelles Belgique Phone: 32-2-650 3001 Fax: 32-2-650 3606 E-mail:cbiot@ulb.ac.be http://babylone.ulb.ac.be/~christophe/ http://www.ulb.ac.be/rech/inventaire/unites/ULB163.html ******************************************************* From chemistry-request@server.ccl.net Thu Sep 26 10:39:03 2002 Received: from sgofims01.ccs.ppg.com ([141.189.251.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8QEd3a03608 for ; Thu, 26 Sep 2002 10:39:03 -0400 Received: by sgofims01.ccs.ppg.com with Internet Mail Service (5.5.2653.19) id ; Thu, 26 Sep 2002 10:39:03 -0400 Message-ID: <2195C52A2E0BD41190CB0090273F72E5043906C5@sgofusr09.ccs.ppg.com> From: "Deng, Jun" To: chemistry@ccl.net Subject: polarizability potential Date: Thu, 26 Sep 2002 10:38:59 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Can anyone suggest some software that can calculate polarizability potential? thank you very much! Jun Deng From chemistry-request@server.ccl.net Thu Sep 26 10:34:19 2002 Received: from dux1.tcd.ie ([134.226.1.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8QEYJa03524 for ; Thu, 26 Sep 2002 10:34:19 -0400 Received: from wallaceiwork (chy108098.phy.tcd.ie [134.226.108.98]) by dux1.tcd.ie (Postfix) with SMTP id 0C15162B for ; Thu, 26 Sep 2002 15:34:01 +0100 (IST) Message-ID: <000c01c2656a$f8620f70$626ce286@wallaceiwork> From: "Iain Wallace" To: "CCL" Subject: CCL: 2D pictures/structure generator Date: Thu, 26 Sep 2002 15:42:32 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C26573.541DAAB0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 This is a multi-part message in MIME format. ------=_NextPart_000_0007_01C26573.541DAAB0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, I have two quick questions if you don't mind: 1) Does any one know of a free program that convert molecules in smiles = format ( or some other format) into a picture, using a command line for = windows. I want to create an excel spreadsheet with a picture of each of = my molecules, by using a simple script.=20 2) Does any one know of a free program that can generate molecules based = on a given fragment. I have a drug molecule, and a protein, and would = like to generate molecules by modifying some of the substituents of the = drug molecule and attempt to dock them. Thanks for any help you can give me Iain=20 ------=_NextPart_000_0007_01C26573.541DAAB0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi all,

I have two quick questions if you don't = mind:

1) Does any one know of a free program = that convert=20 molecules in smiles format ( or some other format) into a picture, using = a=20 command line for windows. I want to create an excel spreadsheet with a = picture=20 of each of my molecules, by using a simple script.

2) Does any one know of a free program = that can=20 generate molecules based on a given fragment. I have a drug molecule, = and a=20 protein, and would like to generate molecules by modifying some of = the=20 substituents of the drug molecule and attempt to dock them.

Thanks for any help you can give = me

Iain

------=_NextPart_000_0007_01C26573.541DAAB0-- From chemistry-request@server.ccl.net Thu Sep 26 14:01:02 2002 Received: from hotmail.com ([64.4.19.106]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8QI12a08311 for ; Thu, 26 Sep 2002 14:01:02 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 26 Sep 2002 11:00:57 -0700 Received: from 129.173.17.185 by lw12fd.law12.hotmail.msn.com with HTTP; Thu, 26 Sep 2002 18:00:56 GMT X-Originating-IP: [129.173.17.185] From: "Zhijian Wu" To: chemistry@ccl.net Subject: solvation energy Date: Thu, 26 Sep 2002 14:00:56 -0400 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 26 Sep 2002 18:00:57.0090 (UTC) FILETIME=[A9F00E20:01C26586]

Hi, cclers,

Does anyone know that for the charged speices (say, +1 and -1), how accurate of the Onsager Model (based on dipole moment) on the solvation energy?

Thank you very much for your help!

Regards,

Zhijian Wu

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From chemistry-request@server.ccl.net Thu Sep 26 23:13:43 2002 Received: from mail.chem.tamu.edu ([165.91.176.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8R3Dha22590 for ; Thu, 26 Sep 2002 23:13:43 -0400 Received: from [165.91.178.2] (account ) by mail.chem.tamu.edu (CommuniGate Pro WebUser 3.5.9) with HTTP id 301837 for ; Thu, 26 Sep 2002 22:12:12 -0500 From: "Yubo Fan" Subject: atlas for P4/AthlonXP To: chemistry@ccl.net X-Mailer: CommuniGate Pro Web Mailer v.3.5.9 Date: Thu, 26 Sep 2002 22:12:12 -0500 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Content-Transfer-Encoding: 8bit Hi, everyone, Is there any specific version of ATLAS compilable for G98A11 on P4 or AnthlonXP? Thanks. Yubo ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================