From chemistry-request@ccl.net Wed Dec 10 18:50:34 2003 Received: from copland.udel.edu (copland.udel.edu [128.175.13.92]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBANo38a001603 for ; Wed, 10 Dec 2003 18:50:03 -0500 Received: from [128.175.138.90] ([128.175.138.90]) by copland.udel.edu (8.12.10/8.12.10) with ESMTP id hBANo1LP016086 for ; Wed, 10 Dec 2003 18:50:01 -0500 (EST) Message-Id: <200312102350.hBANo1LP016086[at]copland.udel.edu> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Wed, 10 Dec 2003 18:42:07 -0500 Subject: g03 and g98, cosmo optimizations From: "Olga Dmitrenko" To: chemistry[at]ccl.net Mime-version: 1.0 X-Priority: 3 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-Spam-Score: 0.9 DEAR_SOMEBODY,SPAM_PHRASE_00_01 X-Scanned-By: MIMEDefang 2.37 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear All, I run my optimization jobs on different sites, one of them has Gaussian03 whereas others have gaussian98. I noticed that energies of structures optimized in water using COSMO are different in g98 and g03. So, it looks to me that COSMO in g98 is not the same COSMO in g03. Am I right with this observation? Which one is better? I am getting very different results for proton affinities using the same geometries (optimized using g03) and using single point g98 calcs. I'll check it again, but I will appreciate to know if somebody already experienced similar problems. Best regards, Olga Dmitrenko P.S. My control card is following: # B3LYP/6-311+G(d,p) freq=noraman fopt scrf=(cosmo,solvent=water) or # TD(50-50,Nstates=6) rb3lyp/6-311+g(d,p) scrf=(solvent=water,cosmo) TD B3lYP should give the same ground state energy as B3LYP if structure is the same. From chemistry-request@ccl.net Thu Dec 11 13:25:46 2003 Received: from hotmail.com (bay13-f110.bay13.hotmail.com [64.4.31.110]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBBIPE8a005747 for ; Thu, 11 Dec 2003 13:25:14 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 11 Dec 2003 10:25:14 -0800 Received: from 202.141.142.20 by by13fd.bay13.hotmail.msn.com with HTTP; Thu, 11 Dec 2003 18:25:13 GMT X-Originating-IP: [202.141.142.20] X-Originating-Email: [vemaparna!at!hotmail.com] X-Sender: vemaparna!at!hotmail.com From: "Aparna Vema" To: chemistry!at!ccl.net Subject: Heme and Zn parmeters Date: Thu, 11 Dec 2003 23:55:13 +0530 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 11 Dec 2003 18:25:14.0088 (UTC) FILETIME=[1E8C0E80:01C3C014] X-Spam-Status: No, hits=1.2 required=7.0 tests=CLICK_BELOW,HTML_30_40,HTML_LINK_CLICK_HERE,HTML_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp)

Dear all,

Can anyone suggest me where can i get amber parameters for

1)Heme in which Fe is co-ordinated to S-atom of Cysteine

2)Zn metal atom co-ordinated to S-atoms of 4 cysteine residues

Sincerely,

Aparna

-------------------------------------------------------------------------------

-Vema Aparna  Research Scholar
Prof. G.R. Desiraju's Group, School of Chemistry
University Of Hyderabad, Hyderabad - 500 046 INDIA

Get the best astro advice. See what the stars hold in store. Simply click here. From chemistry-request@ccl.net Thu Dec 11 13:30:55 2003 Received: from glu.fcfrp.usp.br (glu.fcfrp.usp.br [143.107.202.226]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBBIUN8a006055 for ; Thu, 11 Dec 2003 13:30:24 -0500 Received: from localhost (fabio@localhost) by glu.fcfrp.usp.br (SGI-8.9.3/8.9.3) with ESMTP id QAA54708 for ; Thu, 11 Dec 2003 16:31:52 -0800 (PST) Date: Thu, 11 Dec 2003 16:31:52 -0800 From: Fabio Vasconcelos Figueiredo To: chemistry..at..ccl.net Subject: grasp errors salving file Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I've been using GRASP and this program has problem to save images of eletrostatic maps how showed below: ALERT: grasp [53638] - out of logical swap space during fork/sproc - see swa p(1M) someone has an idea of how to solve this problem? thank's for your answer Fabio Fig. From chemistry-request@ccl.net Thu Dec 11 14:27:04 2003 Received: from mail.ccmsi.us (mccmsi.jsums.edu [143.132.103.55]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBBJQW8a009239 for ; Thu, 11 Dec 2003 14:26:32 -0500 Received: from FALCON [10.30.6.25] by mail.ccmsi.us with ESMTP (SMTPD32-8.03) id A4CD172700F8; Thu, 11 Dec 2003 13:26:05 -0600 From: "Yevgeniy Podolyan" To: Subject: 04.03.26 4th Southern School on Computational Chemistry, Orange Beach, AL, USA Date: Thu, 11 Dec 2003 13:26:27 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0010_01C3BFEA.619CE2F0" X-Mailer: Microsoft Office Outlook, Build 11.0.5510 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Thread-Index: AcPAHKwdo8MAAVgwQrKVg9Uhy63IJA== Message-Id: <20031211132626.SM01804@FALCON> X-Spam-Status: No, hits=5.1 required=7.0 tests=FORGED_MUA_OUTLOOK,HTML_30_40,HTML_MESSAGE, MISSING_OUTLOOK_NAME version=2.55 X-Spam-Level: ***** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0010_01C3BFEA.619CE2F0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Colleague: We invite you to participate in the 4th Southern School on Computational Chemistry organized together by the members of the NSF-EPSCOR Computational Chemistry Cluster, NSF-CREST Computational Center for Molecular Structure and Interactions, and the Army High Performance Computing Research Center. The meeting will be held at the Winfield Resort Hotel in beautiful Orange Beach, Alabama (next to Pensacola, FL) on March 26 and 27, 2004 (Friday 2 p.m. - Saturday 10 p.m.). There will be two formal lectures by Dr. Ernest Davidson from University of Washington and Dr. Andrzej Sadlej from Nicolaus Copernicus University, Poland. In addition, we are planning 20-30-minute oral presentations of senior investigators and posters from the students. These presentations will cover all areas of computational and quantum chemistry. A special session on High Performance Computing on Large Molecular Systems is scheduled for the Friday afternoon. We will publish a volume of proceedings with abstracts and a special issue of "Structural Chemistry" with selected papers from the meeting. Please email your abstracts and your pictures by March 1, 2004 to Dr. Y. Podolyan podolyan..at..ccmsi.us (up to 4 pages in Microsoft Word format). The pictures will be included in the conference materials along with the list of participants. For details on abstract and picture formats, conference program, online registration, and other information visit our conference web site at http://sscc.ccmsi.us . The conference fee, which includes meals (Friday dinner through Sunday breakfast), is $125. I hope to see you at our School. Jerzy Leszczynski ------=_NextPart_000_0010_01C3BFEA.619CE2F0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear=20 Colleague:

We = invite you to=20 participate in the 4th Southern School on Computational = Chemistry=20 organized together by the members of the NSF-EPSCOR Computational = Chemistry=20 Cluster, NSF-CREST Computational Center for Molecular Structure and = Interactions, and=20 the Army=20 High Performance Computing Research Center.

The = meeting will=20 be held at the Winfield Resort Hotel in beautiful Orange Beach, Alabama = (next to=20 Pensacola, FL) on March 26 and 27, 2004 (Friday 2 p.m. – Saturday = 10=20 p.m.).

There = will be two=20 formal lectures by Dr. Ernest Davidson from University of Washington and Dr. Andrzej Sadlej from Nicolaus = Copernicus=20 University, Poland.

In = addition, we=20 are planning 20-30-minute oral presentations of senior investigators and = posters=20 > from the students. These presentations will cover all areas of = computational and=20 quantum chemistry. A special session on High Performance Computing on = Large=20 Molecular Systems is scheduled for the Friday afternoon. We will publish = a=20 volume of proceedings with abstracts and a special issue of "Structural=20 Chemistry" with selected papers from the meeting. Please email your = abstracts=20 and your pictures by March 1, 2004 to Dr. Y. Podolyan podolyan..at..ccmsi.us = (up to 4=20 pages in Microsoft Word format). The pictures will be included in the = conference=20 materials along with the list of participants. For details on abstract = and=20 picture formats, conference program, online registration, and other = information=20 visit our conference web site at http://sscc.ccmsi.us .

The = conference=20 fee, which includes meals (Friday dinner through Sunday breakfast), is=20 $125.

I hope = to see you=20 at our School.

Jerzy=20 Leszczynski

 

------=_NextPart_000_0010_01C3BFEA.619CE2F0-- From chemistry-request@ccl.net Thu Dec 11 18:11:59 2003 Received: from fep01-svc.swip.net (fep01.swip.net [130.244.199.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBBNBR8a021716 for ; Thu, 11 Dec 2003 18:11:28 -0500 Received: from em386 ([213.103.207.143]) by fep01-svc.swip.net with ESMTP id <20031211231127.HMNG3280.fep01-svc.swip.net@em386>; Fri, 12 Dec 2003 00:11:27 +0100 Date: Fri, 12 Dec 2003 00:05:53 +0000 From: "Pascal Bonnet" Reply-To: bonnetpascal/at/libertysurf.fr To: "chemistry/at/ccl.net" , "Aparna Vema" Subject: Re: CCL:Heme and Zn parmeters X-mailer: Foxmail 5.0 beta2 [-fr-] Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====003_Dragon817104848453_=====" Message-Id: <20031211231127.HMNG3280.fep01-svc.swip.net@em386> X-Spam-Status: No, hits=1.7 required=7.0 tests=CLICK_BELOW,HTML_10_20,HTML_LINK_CLICK_HERE,HTML_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. --=====003_Dragon817104848453_===== Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dear Vema, You can found heme parameters from the contributed parameters database maintained by Richard Bryce at: http://pharmacy.man.ac.uk/amber/ Pascal Dear all, Can anyone suggest me where can i get amber parameters for 1)Heme in which Fe is co-ordinated to S-atom of Cysteine 2)Zn metal atom co-ordinated to S-atoms of 4 cysteine residues Sincerely, Aparna ------------------------------------------------------------------------------- -Vema Aparna Research Scholar Prof. G.R. Desiraju's Group, School of Chemistry University Of Hyderabad, Hyderabad - 500 046 INDIA email: vemaparna/at/hotmail.com Get the best astro advice. See what the stars hold in store. Simply click here. -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY/at/ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl/at/ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ --=====003_Dragon817104848453_===== Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: 7bit
Dear Vema,
 
You can  found heme parameters from the contributed parameters database maintained by Richard Bryce at:
 
Pascal
 
 
 

Dear all,

Can anyone suggest me where can i get amber parameters for

1)Heme in which Fe is co-ordinated to S-atom of Cysteine

2)Zn metal atom co-ordinated to S-atoms of 4 cysteine residues

Sincerely,

Aparna

-------------------------------------------------------------------------------

-Vema Aparna  Research Scholar
Prof. G.R. Desiraju's Group, School of Chemistry
University Of Hyderabad, Hyderabad - 500 046 INDIA

Get the best astro advice. See what the stars hold in store. Simply click here. 
-= This is automatically added to each message by the mailing script =-
To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
and send your message to:  CHEMISTRY/at/ccl.net

Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net 
HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs 

If your mail is bouncing from CCL.NET domain send it to the maintainer:
Jan Labanowski,  jkl/at/ccl.net (read about it on CCL Home Page)
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--=====003_Dragon817104848453_=====--