From chemistry-request@server.ccl.net Tue Apr 2 09:09:22 2002 Received: from web21108.mail.yahoo.com ([216.136.227.110]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g32E9Lp10194 for ; Tue, 2 Apr 2002 09:09:21 -0500 Message-ID: <20020402140908.503.qmail@web21108.mail.yahoo.com> Received: from [203.197.89.196] by web21108.mail.yahoo.com via HTTP; Tue, 02 Apr 2002 06:09:08 PST Date: Tue, 2 Apr 2002 06:09:08 -0800 (PST) From: Gurpreet Singh Subject: basis set To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, I am presently running a calculation to determine the electric field gradient tensors for a large organic compound (72 atoms)(dimer 114 atoms) in Gaussian 98. What would be the minimal basis set for determining the efg tensors accurately ? MOreover are there any other public domain sofware available to calculate the efg tensors ? Gurpreet __________________________________________________ Do You Yahoo!? Yahoo! Tax Center - online filing with TurboTax http://http://taxes.yahoo.com/ From chemistry-request@server.ccl.net Mon Apr 1 16:45:36 2002 Received: from dux1.tcd.ie ([134.226.1.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g31Ljap18202 for ; Mon, 1 Apr 2002 16:45:36 -0500 Received: from wallaceiwork (chy108098.phy.tcd.ie [134.226.108.98]) by dux1.tcd.ie (Postfix) with SMTP id 1ADBC5B1 for ; Mon, 1 Apr 2002 22:45:25 +0100 (IST) Message-ID: <000c01c1d9c6$e9a43790$626ce286@wallaceiwork> From: "Iain Wallace" To: Subject: CCL: Preparing Proteins for Docking Date: Mon, 1 Apr 2002 22:48:08 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C1D9CF.4B54C970" 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_0009_01C1D9CF.4B54C970 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all,=20 I was wondering if any one knew of a free program that can prepare = proteins for docking calculations.=20 By this I mean, a program that can add add missing/polar Hydrogens, and = assign charges to a pdb file.=20 Thanks=20 Iain=20 ------=_NextPart_000_0009_01C1D9CF.4B54C970 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi all,

I was wondering if any one knew of a = free program=20 that can prepare proteins for docking calculations.

By this I mean, a program that can = add add=20 missing/polar Hydrogens, and assign charges to a pdb file.

Thanks

Iain

------=_NextPart_000_0009_01C1D9CF.4B54C970-- From chemistry-request@server.ccl.net Mon Apr 1 10:52:32 2002 Received: from mail.iitk.ac.in ([203.200.95.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g31FqUp11180 for ; Mon, 1 Apr 2002 10:52:30 -0500 Received: from antivirus.cc.iitk.ac.in (antivirus.cc.iitk.ac.in [172.31.1.102]) by mail.iitk.ac.in (8.9.3+Sun/8.9.3) with SMTP id VAA00328 for ; Mon, 1 Apr 2002 21:22:30 +0530 (IST) Received: (from bhaskar [172.31.1.7]) by antivirus.cc.iitk.ac.in (NAVGW 2.5.1.6) with SMTP id M2002040121500519694 for ; Mon, 01 Apr 2002 21:50:05 +0530 Date: Mon, 1 Apr 2002 21:21:09 +0530 (IST) From: "97104 Chinmoy Ranjan UG(CHM)." X-Sender: ranjan@bhaskar.cc.iitk.ac.in To: CHEMISTRY@ccl.net Subject: g98 prob with scipcm Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I am trying to a single point energy calculation using the ] SCIPCM model. The calculation terminates with. . Compute SCI-PCM surface. WARNING! Serious error in surface integrals. It is probable that some of the solute is outside the cavity and/or arts of the cavity surface cannot be reached from the origin. Try more integration points or a different set of integration origins. Surface Problems in SciFoc Error termination via Lnk1e in /usr1/sm/gaussian98/g98/l502.exe. Job cpu time: 0 days 0 hours 30 minutes 0.1 seconds. File lengths (MBytes): RWF= 58 Int= 0 D2E= 0 Chk= 19 Scr= 1 I have gone through similar postings in the CCL archives but without any solution. Any kind suggesstion is highly appreciated. with regards Chinmoy Ranjan ****************************************************************************** CHINMOY RANJAN | Permanent Address: A-216 HALL 1 | D-9, Nehru Shatabdi Central Hospital, INDIAN INSTITUTE OF TECHNOLOGY | Talcher, Post- Dera, pin code - 759103 KANPUR - 208016 | Distt- Angul, U.P | Orissa. INDIA | INDIA | email: ranjan@iitk.ac.in chinmoyranjan@hotmail.com No matter what conditions you encounter in life, your right is only to the works--not to the fruits thereof. You should not be impelled to act for selfish reasons, nor should you be attached to inaction. -Bhagavad Gita ****************************************************************************** From chemistry-request@server.ccl.net Mon Apr 1 14:18:02 2002 Received: from sina.iums.ac.ir ([194.225.184.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g31JHwp16231 for ; Mon, 1 Apr 2002 14:17:59 -0500 Received: from amsh0me.iums.ac.ir ([194.225.184.135]) by sina.iums.ac.ir (8.9.2/8.9.2) with ESMTP id XAA22818; Mon, 1 Apr 2002 23:49:41 +0330 (IST) Message-Id: <5.0.2.1.2.20020401233141.00b5acc8@sina.iums.ac.ir> X-Sender: armin@sina.iums.ac.ir X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Mon, 01 Apr 2002 23:44:43 +0430 To: CHEMISTRY@ccl.net From: "Armin M. Sobhani" Subject: Re: CCL:Linux/x86 compiler question Cc: Joe Huang In-Reply-To: <3CA896F7.8060305@uh.edu> References: <5.0.2.1.2.20020331143030.00b5f0e8@sina.iums.ac.ir> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed On Monday, 1 April 2002, Hung-Chung (Joe) Huang wrote: >Thanks for your valuable and useful information. >But, I could not find that non-commercial version of both compilers for >RedHat Linux you mentioned in your message; I could only find the free >evaluation version that will be expired after one month once you install >it. When did you get that free non-commercial version? Is the version you >got the same as the evaluation version? >Your help will be much appreciated! In case others have the same problem, here are URLs for non-commercial versions of Intel's C/C++ and Fortran compilers for RedHat Linux respectively: http://developer.intel.com/software/products/compilers/c50/linux/noncom.htm http://developer.intel.com/software/products/compilers/f50/linux/noncom.htm Please note that these versions cannot be used to produce software for resale and commercial use. Armin p-----__---_________----____----------------------------------------q | / \ / _ _ \ / ____\ Armin M. Sobhani, PharmD, PhD | | / \\ \\ \\ \/\ \___/_ Assitant Prof., Pharmacology Dept. | | / /\ \\ \\ \\ \ \_____ \ Iran University of Medical Sciences| | ( ___ \\ \\ \\ \/____/\ \ mailto:armin@iums.ac.ir | |( \__\_/\__\\__\\__\\__\/\_____/ Tel: +98 (21) 805 2265, Fax: ~64 | | \/__/ \/__//__//__//__/\/____/ P.O.Box: 14155-6183, Tehran, IRAN | |~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| | Once you understand the universe at the atomic level everything | | else is easy. -Richard P. Feynman | b-------------------------------------------------------------------d From chemistry-request@server.ccl.net Tue Apr 2 14:09:02 2002 Received: from yakko.cimav.edu.mx ([148.223.46.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g32J91p18438 for ; Tue, 2 Apr 2002 14:09:01 -0500 Received: from glossman (mild.cimav.edu.mx [148.223.46.1]) by yakko.cimav.edu.mx (8.11.6/8.11.2) with SMTP id g32Jjw225947 for ; Tue, 2 Apr 2002 12:45:58 -0700 Message-ID: <006201c1da80$0767d980$2601010a@cimav.edu.mx> From: "Dr. Daniel Glossman-Mitnik" To: "Computational Chemistry List" Subject: g98 compilation on sgi solved!!! Date: Tue, 2 Apr 2002 11:53:15 -0800 Organization: CIMAV - LAQUICOM MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear netters: Thank you all who answered my question about the compilation problem of G98 on SGI. As many of you (including Doug Fox, > from Gaussian) stated, the supported compilers are versions 7.3. So I upgraded from 7.0 to 7.3 and the compilation ran smooth. Thanks again Dr. Daniel Glossman-Mitnik PS: There was one question about what compiler I have used for Linux Red Hat 7.2. I have used the Fortran 77 compiler from Portland and I have no experience with free compilers. ************************************************************************** Dr. Daniel Glossman-Mitnik Centro de Investigacion en Materiales Avanzados (CIMAV) LAQUICOM - Laboratorio de Química Computacional Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - Mexico Phone: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman@cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com ************************************************************************** From chemistry-request@server.ccl.net Tue Apr 2 11:58:22 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g32GwMp15284 for ; Tue, 2 Apr 2002 11:58:22 -0500 Received: from cornell.edu (phobos.mbg.cornell.edu [132.236.170.77]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id LAA06100; Tue, 2 Apr 2002 11:58:16 -0500 (EST) Sender: richard@cornell.edu Message-ID: <3CA9E5F7.2918281F@cornell.edu> Date: Tue, 02 Apr 2002 12:10:15 -0500 From: Richard Gillilan Reply-To: reg8@cornell.edu X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16-3 i686) X-Accept-Language: en MIME-Version: 1.0 To: Iain Wallace CC: chemistry@ccl.net Subject: Re: CCL:Preparing Proteins for Docking References: <000c01c1d9c6$e9a43790$626ce286@wallaceiwork> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Iain Wallace wrote: > Hi all, I was wondering if any one knew of a free program that can prepare proteins for docking calculations.By this I mean, a program that can add add missing/polar Hydrogens, > and assign charges to a pdb file. Reduce can add hydrogens and optimize the positions. I have been able to compile it on both Linux and MacOS X, but I have not actually used it: http://kinemage.biochem.duke.edu/software/softdocs/README.reduce.html If you can produce a mol2 file, you could use my program OrderFour to assign MMFF94 charges to the protein. OrderFour will also remove non-polar hydrogens below any given charge cutoff. Problem is that you need correct bond orders in the mol2. In the past I've used InsightII to get these .. I'd love to have a better way to generally add all hydrogens and determine bond orders. Richard From chemistry-request@server.ccl.net Tue Apr 2 14:32:36 2002 Received: from toni.schrodinger.com ([192.156.98.56]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g32JWZp18816 for ; Tue, 2 Apr 2002 14:32:35 -0500 Received: (from announce@localhost) by toni.schrodinger.com (8.8.8/8.8.5) id LAA18826 for chemistry@ccl.net; Tue, 2 Apr 2002 11:32:25 -0800 Message-Id: <200204021932.LAA18826@toni.schrodinger.com> Subject: Leadership in Drug Discovery: Setting New Standards in Structure-based Drug Design To: chemistry@ccl.net Date: Tue, 2 Apr 2002 11:32:25 -0800 (PST) From: Schrodinger Announce Account Reply-To: Schrodinger Information Account X-Mailer: ELM [version 2.5 PL0b2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Schrodinger cordially invites you to "Leadership in Drug Discovery: Setting New Standards in Structure-based Drug Design", a half-day seminar on recent breakthroughs in drug design and virtual screening. Please join us for a morning of talks featuring top scientists from well-known pharmaceutical and biopharmaceutical companies who will discuss current challenges and how to address them. Seminars will be hosted in two locations on the East coast and two locations on the West coast on the dates and locations listed below. Seminars will run > from 9:00 AM - 1:00 PM. Complimentary breakfast and lunch will be served at all events. Please take a moment to reserve a place by calling Robert Distifeno, 503-299-1150 Ext. 123 or filling out the form at http://www.schrodinger.com/Announce/Workshop/W2002/new_standards.html Seminar Dates and Locations: Thursday, April 25, 2002 Princeton, NJ Tuesday, April 30, 2002 San Diego, CA Thursday, May 2, 2002 San Francisco, CA Tuesday, May 7, 2002 Research Triangle Park, NC ------------------------------------------------------------------- If you do not wish to receive future e-mail announcements from Schrodinger, Inc., please send a message to remove@schrodinger.com. From chemistry-request@server.ccl.net Tue Apr 2 17:30:09 2002 Received: from chem-mail.chemistry.gatech.edu ([130.207.35.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g32MU9p22806 for ; Tue, 2 Apr 2002 17:30:09 -0500 Received: from cicero.chemistry.gatech.edu (cicero.chemistry.gatech.edu [130.207.35.109]) by chem-mail.chemistry.gatech.edu (8.9.0/8.9.0) with ESMTP id RAA26860 for ; Tue, 2 Apr 2002 17:52:45 -0500 (EST) Date: Tue, 2 Apr 2002 17:28:35 -0500 (EST) From: David Sherrill To: Subject: Southeast Theoretical Chemistry Assoc, May 24-25, Atlanta Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The 2002 meeting of the Southeast Theoretical Chemistry Association (SETCA) will be held on the Georgia Tech Campus in Atlanta, Georgia on May 24-25. Please check out the website at http://vergil.chemistry.gatech.edu/setca2002/ for all the details including registration. (The cost of the meeting will be $40/person, and includes the banquet on Friday night.) The meeting will include 9 plenary lectures, 6 contributed talks, and a poster session. As of this writing, the confirmed speakers include: Joel Bowman, Emory University Daniel Crawford, Virginia Tech Michael Herman, Tulane University James Kindt, Emory University Jeff Krause, University of Florida Keiji Morokuma, Emory University Fritz Schaefer, University of Georgia Steve Stuart, Clemson University Please feel free to pass this message on to others who you think might be interested in attending. We look forward to seeing you and/or your students in Atlanta in about two months! Regards, Rigoberto Hernandez C. David Sherrill Edward Valeev